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Modelling osteomyelitis
Pietro Liò1, Nicola Paoletti2*, Mohammad Ali Moni1, Kathryn Atwell1, Emanuela Merelli2, Marco Viceconti3
From NETTAB 2011 Workshop on Clinical Bioinformatics
Pavia, Italy. 12-14 October 2011
Abstract
Background: This work focuses on the computational modelling of osteomyelitis, a bone pathology caused by
bacteria infection (mostly Staphylococcus aureus). The infection alters the RANK/RANKL/OPG signalling dynamics
that regulates osteoblasts and osteoclasts behaviour in bone remodelling, i.e. the resorption and mineralization
activity. The infection rapidly leads to severe bone loss, necrosis of the affected portion, and it may even spread to
other parts of the body. On the other hand, osteoporosis is not a bacterial infection but similarly is a defective
bone pathology arising due to imbalances in the RANK/RANKL/OPG molecular pathway, and due to the
progressive weakening of bone structure.
Results: Since both osteoporosis and osteomyelitis cause loss of bone mass, we focused on comparing the
dynamics of these diseases by means of computational models. Firstly, we performed meta-analysis on a gene
expression data of normal, osteoporotic and osteomyelitis bone conditions. We mainly focused on RANKL/OPG
signalling, the TNF and TNF receptor superfamilies and the NF-kB pathway. Using information from the gene
expression data we estimated parameters for a novel model of osteoporosis and of osteomyelitis. Our models
could be seen as a hybrid ODE and probabilistic verification modelling framework which aims at investigating the
dynamics of the effects of the infection in bone remodelling. Finally we discuss different diagnostic estimators
defined by formal verification techniques, in order to assess different bone pathologies (osteopenia, osteoporosis
and osteomyelitis) in an effective way.
Conclusions: We present a modeling framework able to reproduce aspects of the different bone remodeling
defective dynamics of osteomyelitis and osteoporosis. We report that the verification-based estimators are
meaningful in the light of a feed forward between computational medicine and clinical bioinformatics.
© 2012 Liò et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.
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signals that flow through the osteocytic canalicular net- lining cells pull away from the bone matrix, forming
work to the BMU cells. In normal bone, the number of a canopy which merges with the blood vessels.
BMUs, the bone resorption rate, and the bone formation 2. Osteoclast recruitment. Stromal cells divide and
rate are all relatively constant [3]. differentiate into osteoblasts precursors. Pre-osteo-
The RANK/RANKL/OPG signalling pathway plays an blasts start to express RANKL, inducing the differen-
important role in bone metabolism. RANK is a protein tiation of and attracting pre-osteoclasts, which have
expressed by osteoclasts; RANK is a receptor for RANK receptors on their surfaces. RANKL is a
RANKL, a protein produced by osteoblasts. RANK/ homotrimeric molecule displayed on the membrane
RANKL signalling triggers osteoclast differentiation, pro- of osteoblasts that stimulates differentiation in osteo-
liferation and activation, thus it prominently affects the clasts and is a key induction molecule involved in
resorption phase during bone remodelling. Osteoprote- bone resorption leading to bone destruction.
gerin (OPG) is a decoy receptor for RANKL. It is 3. Resorption. The pre-osteoclasts enlarge and fuse
expressed by mature osteoblasts and it binds to RANKL, into mature osteoclasts. In cortical BMUs, osteo-
thus inhibiting the production of osteoclasts. Figure 1 clasts excavate cylindrical tunnels in the predomi-
shows the key steps during the bone remodelling pro- nant loading direction of the bone, while in
cess, that are: trabecular bone they act at the bone surface, digging
a trench rather than a tunnel. After the resorption
1. Origination. During normal turnover or after a process has terminated, osteoclasts undergo
micro-crack, or as a response to mechanical stress, apoptosis.
the osteocytes in the bone matrix produce biochem- 4. Osteoblast recruitment. Pre-osteoblasts mature
ical signals showing sufferance towards the lining into osteoblasts and start producing osteoprotegerin
cells, i.e. the surface cells around the bone. The (OPG). OPG inhibits the osteoclastic activity by
Figure 1 Key steps in bone remodelling. 1) Osteocytes send signals to the fluid part, activating pre-osteoblasts (Pb) and pre-osteoclasts (Pc). 2)
Pbs express RANKL and Pcs express the RANK receptor. 3) RANK/RANKL binding induces Pcs’ proliferation. Pcs enlarge and fuse, forming mature
osteoclasts which start the bone resorption process. 4) Mature osteoblasts express the decoy receptor OPG and start the bone formation
process. RANKL/OPG binding inhibits RANKL, thus protecting bone from excessive resorption. 5) During the mineralization process, osteoids
secreted by osteoblasts calcify. 6) Finally in the resting phase, the initial situation is re-established.
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We have compared the expression levels of genes involved become more deregulated in both osteomyelitis and
in osteomyelitis, osteoporosis patients and healthy controls osteoporosis. There is the increased expression of differ-
using the box plots and comparison table (Figure 2, 3 and ent isoforms of OPG which are known to have different
Table 1). We report in Table 1 the significant genes asso- binding capability with RANKL and seem to be linked,
ciated with the infection of osteomyelitis and or with the from mice experiments, to hypocalcemia [9]. Therefore
condition of osteoporosis. From the analysis of our data, we report that gene expression in osteoporosis and
we observe that few genes, related to TNF, TNF receptor osteomyelitis could generate an unbalance between
superfamilies and to NF-kB have statistically different RANKL and OPG due to the different OPG isoforms,
levels of expression in healthy controls, osteomyelitis and but also other genes, related to TNF, TNF receptor
or osteoporosis. We observe that, with respect to control superfamilies and to NF-kB may be involved. Although
cases, for the microarray platform GPL96, 22 genes related gene expression and actual protein abundance are only
to RANKL, RANK, OPG, NF-kB proteins, TNF and TNF loosely correlated, taking into account the results of
receptor superfamilies are over expressed and 13 genes are gene expression data, we modified the autocrine and
down regulated in osteomyelitis (see Figure 2 and Table paracrine parameters of the existing mathematical
1). There are other 47 genes that are weakly correlated model based on Komarova model [10]. We considered
with this infection (not shown). However, in case of more appropriate to incorporate into the model the
GPL97 microarray platform, only 10 genes are highly algebraic relationship of positive and negative regulators
expressed; 6 genes are down expressed (other 15 genes are (such as RANKL and OPG) than just the RANKL
weakly correlated in osteomyelitis) (see Figure 3 and Table change. On the basis of this consideration we developed
1). For the osteoporosis condition, using the platform new models for reproducing osteoporotic and osteomye-
GPL96, only 10 genes are up regulated and 6 are down litis conditions.
regulated (see Table 1). It is notable in the platform
GPL96, only 4 genes NFKB2_1, NFKB2_2, REL_2 and A computational framework for bone dynamics
RELB are up-regulated in both types of diseases. In con- In this work we present a combined computational fra-
trast, only 3 genes TNFRSF25_2, TRAF3IP3_1 and TRAF5 mework for the modelling, simulation and verification of
are down regulated in the both osteomyelitis infection and the bone remodelling process, and of bone pathologies
osteoporosis. However, 5 genes NFKB1, RELA_1, like osteomyelitis and osteoporosis. Based on the meth-
TNFRSF10B_2, TNFSF10_3 and TRAF3IP3_3 are differ- ods developed in [11,12], this approach consists of the
ently regulated in osteomyelitis and osteoporosis. following two building blocks:
Interestingly we found that, despite a very small Mathematical model
increase of RANKL gene expression in osteoporosis and We develop a differential equation model for describing
a larger increase in osteomyelitis, OPG gene expression the dynamics of bone remodelling and of bone-related
Figure 2 Box plot representation of the gene expression of 82 genes corresponding to a) 48 osteomyelitis infected patients and b) 27
healthy controls).
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Figure 3 Box plot representation of the gene expression of 31 genes corresponding to a) 43 osteomyelitis infected patients and b) 17
healthy controls).
pathologies at a multicellular level. The model describes osteoblasts and osteoclasts, similarly to Ayati’s model on
the continuous changes of, and the interactions between bone myeloma [16]. Although several efforts have been
populations of osteoclasts and osteoblast (including bac- made in developing mathematical model for osteomyeli-
teria in the osteomyelitis model). Bone density is calcu- tis and osteoporosis, molecular data has been rarely con-
lated as the difference between the formation activity sidered so far, regardless the availability of different gene
which is proportional to osteoblasts concentration, and expression microarray data related to osteomyelitis and
the resorption activity which is proportional to osteo- osteoporosis and based on only single microarray data-
clasts concentration. In the last twenty years, a variety base. So, we have developed mathematical model and
of mathematical and computational models has been showed the comparative study of gene expression data
proposed in order to better understand the dynamics of from different databases of similar platform to find out
bone remodelling (reviewed in [13-15]). Three main the genes expression level related to the RANKL,
categories of models can be distinguished: those focus- RANK, OPG and NF-kB proteins, which are strongly
ing on the organ level, where bone is described as a related to the osteomyelitis and osteoporosis.
continuum material only characterized by its density; on Model verification
the biomechanical properties and on the microstructural We define a stochastic model for bone remodelling from
information at the tissue level; and on the cellular level the ODE specification, that allows us to analyse the ran-
where the interactions occurring among the different dom fluctuations and the discrete changes of bone den-
types of bone cells are concerned. The latter category sity and bone cells. Given that randomness is an inherent
can also incorporate intracellular signalling pathways feature of biological systems, whose components are
and mechanosensing mechanisms (i.e. the process by naturally discrete, the stochastic approach could give use-
which mechanical stimuli are translated into cellular sig- ful insights on the bone remodelling process. Indeed, sto-
nals). Our cellular-level model is based on the work by chasticity plays a key role in bone remodelling, e.g. the
Komarova et al [10], where they developed an important fluctuations in molecular concentrations of RANKL and
model for BR based on experimental results described OPG produce changes in the chemotaxis (the process by
in Parfitt’s work [8] which has inspired many other simi- which cells move toward attractant molecules) of osteo-
lar models. In particular we extended it in order to clasts and osteoblasts. This may affect for example the
explicitly simulate bone pathologies: osteoporosis is cell differentiation, number and arrival time, and conse-
reproduced by including an ageing factor that decreases quently the whole remodelling process. Besides achieving
the death rates of cells and by including a factor that a good fitting between the ODE model and the stochastic
increases the RANKL expression; osteomyelitis is mod- one, we employ probabilistic model checking techniques
elled by adding a state variable for bacteria that affects for deriving three different clinical estimators that enable
the autocrine and paracrine regulation factors of to assess the expected bone density, the density change
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Table 1 Comparative representation of gene expression level for osteomyelitis and osteoporosis.
Regulation for Osteomyelitis Gene ID Regulation for Osteomyelitis Gene ID Regulation for Osteoporosis Gene ID
(GPL96) (GPL97) (GPL96)
Up regulated NFKB2_1 Up regulated NFKB2_1 Up regulated NFKB1
NFKB2_2 NFKBIZ_1 NFKB2_1
NFKBIA NFKBIZ_2 NFKB2_2
NFKBIE RELL1 REL_2
REL_2 RELT RELA_1
RELB TNFSF13B_1 RELA_2
TNFRSF10B_2 TNFSF13B_2 RELB
TNFRSF10C_2 TRAF7_1 TNFRSF17
TNFRSF10C TRAF7_3 TNFSF10_2
_3
TNFRSF10C_4 TRAFD1_2 TRAF3_1
TNFRSF1A Down regulated TNFRSF10A Down regulated TNFRSF10B_2
TNFRSF1B TNFRSF18_2 TNFRSF25_2
TNFSF10_1 TRAF1 TNFSF10_3
TNFSF10_2 TRAF3IP1 TRAF3IP3_1
TNFSF10_3 TRAF3IP3_1 TRAF3IP3_3
TNFSF12_3 TRAF3IP3_2 TRAF5
TNFSF12_4
TNFSF12_2
TNFSF13
TRAF3IP3_2
TRAF3IP3_3
TRAFD1_2
Down regulated IKBKG 2
NFKB1
RELA_1
TNFRSF14
TNFRSF25_1
TNFRSF25_2
TNFRSF25_3
TNFRSF25_4
TNFRSF25_6
TRAF1
TRAF3IP2_2
TRAF3IP3_1
TRAF5
rate, and the variance of bone density. Model checking is the graphs produced by simulations towards more pre-
a static technique for automatically search for a property cise quantitative interpretations.
(specified as a logical formula) to hold or not over a defi-
nite set of states, and relies on qualitative properties: Modelling bone remodelling pathologies
given a model and a property to verify, it returns an affir- The ODE model for bone remodelling is mainly inspired
mative or a negative answer, i.e. the property holds or from the work by Komarova et al [10], and describes the
not. Differently, probabilistic model checking is equipped dynamics of osteoblasts’ (Ob) and osteoclasts’ (Oc)
with quantitative information, and given a stochastic population in a BMU, and calculates the bone density as
model and a property to verify, it returns the probability a function of Ob and Oc with the following equations:
of the formula being satisfied. We believe that this kind
of quantitative, formal and automated analysis may dOc g g
= α1 Oc 11 Ob21 − β1 Oc ,
represent a step ahead in the understanding of bone dis- dt
eases like osteomyelitis and osteoporosis, by shifting the dOb g g
= α2 Oc 12 Ob22 − β2 Ob .
attention from an informative, but empirical, analysis of dt
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The model describes the autocrine and paracrine rela- further parameter g por has been included as a factor
tionships between osteoclasts and osteoblasts. Autocrine incrementing g21, in order to incorporate the changes in
signalling usually occurs by a secreted chemical interact- the system RANKL, OPG associated to osteoporosis.
ing with receptors on the surface of the same cell. In The resulting equations for osteoclasts and osteoblasts
the paracrine process a chemical signals that diffuse out- are:
side the emitting cell and interacts with receptors on
nearby cells. Here the parameters gij describe the effec- dOc g g21 +g
= α1 Oc 11 Ob por − gageing β1 Oc ,
tiveness of autocrine and paracrine regulation, s.t. g11 dt
describes the osteoclast autocrine regulation, g 22 the dOb g g
= α2 Oc 12 Ob22 − gageing β2 Ob .
osteoblast autocrine regulation, g 21 is the osteoblast- dt
derived paracrine regulation, and g12 is the osteoclast
paracrine regulation. The nonlinearities of these equa-
Osteomyelitis effects on bone remodelling
tions are approximations for the interactions of the
Starting from the above model of bone remodelling, we
osteoclast and osteoblast populations in the proliferation
consider the progressing of osteomyelitis induced by the
terms of the equations. The autocrine signalling has a
S. aureus (variable B). Since several evidences show that
positive feedback on osteoclast production ( g11 >0), and
the dynamics of the bacterial population follows a Gom-
paracrine signalling has a negative feedback on osteo-
pertz curve, we consider an equation of the form
clast production ( g21 <0). The autocrine signalling has a
positive feedback on osteoblast production ( g22 >0), and dB s
paracrine signalling has a positive feedback on osteoblast = γB B · log( ),
dt B
production ( g12 >0).
Overall the regulatory circuit should lead to a positive where gB is the growth rate of bacteria, and s is the
mineralisation balance (z) which could be described by carrying capacity, i.e. the maximum population size.
dt = −k1 Oc + k2 Ob
the expression dz where k1 and k 2 are Additionally, we introduced four parameters fij used to
the resorption and formation rates, respectively. More model the effects of the infection on the autocrine and
precisely, the bone density is determined by the differ- paracrine regulation factors gij. The resulting equations
ence between the actual resorption and formation activ- are:
ity when osteoclasts and osteoblasts exceed their steady B B
levels. Therefore bone density is calculated as follows: dOc g11 (1+f11 s ) g21 (1+f21 s )
= α1 Oc Ob − β 1 Oc ,
dt
dz B B
dOb g12 (1+f12 s ) g22 −f22 s )
= −k1 max(Oc − Ōc , 0) + k2 max(Ob − Ōb , 0), = α2 Oc Ob − β 2 Ob ,
dt dt
dB s
where Ōc and Ōb denote the steady states of Oc and = (γB − V)B · log( ).
dt B
Ob, resp. For the spongy type bone we consider the vari-
able z as the localized trabecular mass beneath a point This model has been inspired from Ayati’s work on
on the bone surface. multiple myeloma bone disease [16] and the key differ-
In order to reproduce the defective dynamics (i.e. ence with respect to Komarova’s model [10] is the addi-
bone negative balance) characterizing osteoporosis, we tion of the terms fijB/s that couple the bacterial density
assumed an increased death rate for osteoclasts and and its maximum size to the power laws for the osteo-
osteoblasts, motivated by the fact that the occurrence of clast/osteoblast interactions. The bacterial parameters
defective bone pathologies in elderly patients is partly f11, f12, f21, f22 are all nonnegative. The S. aureus-induced
attributable to the reduced cellular activity typical of infection affects the normal remodelling activity by:
those patients. Therefore we introduced the parameter
gageing as a factor multiplying the death rates bi. • reducing osteoblasts’ growth rate: in fact, the
On the other hand, we modified the regulation factors paracrine promotion of osteoblasts is reduced
in order to model an increased RANKL expression by (g12 /(1 + f12 Bs ) < g12 , since g12 > 0) , and the auto-
osteoblasts, which results both from the analysis per- crine promotion of osteoblasts is reduced as well
formed on gene expression data and from experimental (g22 − f22 Bs < g22 ) ;
evidences [6]. In our model g21 is the result of all the • increasing RANKL and decreasing OPG expression:
factors produced by osteoblasts that activates osteoclasts as previously stated, the paracrine inhibition of osteo-
and as explained in [10], g 21 = RANKL OPG where clasts is a negative exponent resulting from the differ-
RANKL is the effectiveness of RANKL signalling while ence between the effectiveness of OPG signalling and
OPG is the effectiveness of OPG signalling. Therefore a that of RANKL signalling. Since g21 (1 − f21 Bs ) > g21 ,
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the infection causes an increase in RANKL expression dosage times t treat = 200, 400 and 600 days. Figure 5
and therefore a decrease in OPG expression. shows that when applying the bacteriostatic drug (e.g.
fusidic acid), the severe bone loss characterizing osteo-
In addition the infection increases the autocrine pro- myelitis can be limited only if the treatment is adminis-
motion of osteoclasts (since g11 >0). We have taken gB to tered at t = 200 days. With later dosages the normal
be independent of bone loss. The parameter V describes remodelling activity cannot be re-established, even if
the effectiveness of the antibiotic treatment as a factor the situation is considerably better w.r.t. an untreated
decreasing the growth rate gB of bacteria. Two different infection. Conversely, the bacteriocide treatment looks
kinds of treatment can be distinguished: bacteriostatic more effective than the bacteriostatic one, and the
treatments that stop bacteria proliferation (V = gB); and bone activity is able to recover regardless the dosage
bacteriocide treatments which kill bacteria (V > gB). time. However the recovery time becomes longer as
Parameters for the three different models (control, ttreat increases. Therefore in both antibiotic treatments
osteoporosis and osteomyelitis) are given in Table 2. timeliness is a crucial factor in order to effectively
Simulation results for bone density, osteoblasts and operate against the infection.
osteoblasts under the three different scenarios are com-
pared in Figure 4. The plots show that both osteoporosis Stochastic model for the verification of bone pathologies
and osteomyelitis are characterized by a negative remo- Following and extending the work in [11], we define a
delling balance, but in the latter case the bone loss stochastic model for bone remodelling and perform for-
becomes much more critical after 600 days. In the mal analysis by means of probabilistic verification tech-
osteoporotic case, the remodelling period is shorter than niques, which allow to assess the probability of a
in the control case, mimicking the fact that in older particular configuration of the biological system (usually
patients microfractures and consequently remodelling expressed as a logical formula) being reached. In our
occur more frequently, in a vicious cycle that progres- settings we derive a Continuous Time Markov Chain
sively weakens the structure and density of the bone [4]. (CTMC) from the mathematical model described above
On the other hand, the regular cycles of the normal and we use the model checker PRISM [17].
bone model above are perturbed by the presence of the We follow a population-based approach where a state
infection (chronic), and we observe longer and unstable of the system is determined by the discrete density of
remodelling periods. the different cell populations involved. Osteoclasts,
Furthermore we simulate the dosage of a bacterio- osteoblasts and bacteria populations are specified as
static treatment (V = 0.005 = gB) and of a bacteriocide PRISM modules, consisting of a random state variable
treatment (V = 0.007 >g B ) for S. Aureus at different modelling the number of individuals; and with a list of
Figure 4 Simulation results of the ODE model. Bone density (first row), number of osteoblasts (second row), and number of osteoclasts (third
row) compared between control and osteoporotic (first column); control and osteomyelitis (second column); osteoporotic and osteomyelitis
(third column). Red lines mark the steady states for the variables considered. Results show a negative remodelling balance in the osteoporotic
case and much more critical in the osteomyelitis case. While we observe a higher (but constant) remodelling rate in the osteoporotic
configuration, in the osteomyelitis scenario the remodelling period is unstable and longer.
stochastic transitions in a guarded-command syntax of where label is an optional transition label; guard is a
the form predicate over the state variables determining whether a
transition is enabled or not; in the CTMC settings, rate
[label] guard → rate : update is the speed/propensity of the action, giving rise to an
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Figure 5 Simulation of a bacteriostatic (V = 0.005 = gB) and a bacteriocide (V = 0.007 >gB) treatment for S. Aureus at different dosage
times (200, 400 and 600 days). Dots on the plots mark the points when treatment is given. As regards the bacteriostatic drug, the bone
density is not subject to critical drops if the treatment is administered at t = 200 days; in the other cases, the normal remodelling activity cannot
be re-established, even if the bone loss is less critical w.r.t. the untreated infection. On the other hand, the bacteriocide treatment looks more
effective than the bacteriostatic one, although recovering the normal density becomes much more difficult if the drug is administered later than
t = 400 days.
exponentially distributed duration of the transition with state variable, but by means of transition rewards, i.e.
mean 1/rate (faster action have a higher probability of positive costs associated to transitions. We implement a
being taken than slower one); and update optionally sets couple (boneFormed, boneResorbed) of rewards asso-
new values to state variables. The ODE model is trans- ciated to osteoblasts’ and osteoclasts’ transitions where
lated into a set of PRISM guarded commands by apply- their stochastic rate is the formation rate (k2Ob) and the
ing the following method [18]. Consider a simple ODE resorption rate (k1Oc), respectively (see Table 3).
dt = α − β
population model of the form dx . The corre-
sponding PRISM transitions would be: Potentialities in clinical bioinformatics and conclusions
Osteomyelitis and osteoporosis are assessed through the
x < xmax → α : x = x + 1 verification of quantitative properties over the defined
x < xmin → β : x = x − 1 stochastic model.
Let assume that the simulation of the PRISM imple-
where xmax and xmin are the maximum and the mini-
mentation of the model is run in parallel with the deter-
mum x, resp. In other words, growth rates in the ODE
mination of clinical parameters during the periodic
model become the stochastic rates in a transition incre-
medical visits of a patient. These medical visits provide
menting the population size, while death rates are
a mean of fine tuning a personalised model of the dis-
involved in the transitions decrementing the population
ease and a measure of how a therapy is effective. Differ-
size.
ent diseases, when monitored in a continuous way, may
Table 3 summarizes the transitions of osteoclasts,
produce different alterations in local mineral density.
osteoblasts and bacteria in the PRISM model. Moreover,
We could extend the statistical estimators of a disease
in order to reduce the state-space of the stochastic
to: 1) the BMD (measured as z-score, the number of
model, bone density has not been implemented as a
standard deviations above or below the mean for the
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[] Oc > 0 ® gageingb1Oc : Oc = Oc - 1
[resorb] Oc > 0 ® k1Oc : true
(b) Osteoblasts
B B
[] 0 < Ob < Obmax Oc > 0 → g12 (1+f11 s ) g22 −f22 s ) : Ob = Ob + 1
α2 Oc Ob
[] Ob > 0 ® gageing b2Ob : Ob = Ob - 1
[form] Ob > 0 ® k2Ob : true
(c) Bacteria
patients age, sex and ethnicity; or as t-score, i.e. the fBD (t) : R{bone Formed} =?[C ≤t ] − R{bone Resorbed} =?[C ≤t ], t = 0, 10, ..., 1200
number of standard deviations above or below the mean
for a healthy 30 year old adult of the same sex and eth-
• Density change rate. It allows to assess rapid
nicity as the patient); 2) The rate of change of BMD.
negative and positive changes in bone density. This
This estimator tells us the emergence of defects of the
estimator could be particularly helpful in detecting
bone metabolism in terms of signaling networks of
the insurgence of osteomyelitis before critical values
RANK/RANKL and decrease of pre-osteoblast number;
of bone density are reached, since osteomyelitis is
3) The variance, skewness and curtosis of the the local
typically characterized by a higher negative change
small scale intermittency of the signal. For example
rate than osteoporosis. In particular the estimator is
osteomyelitis and osteoporosis show slightly confound-
defined as the difference quotient of BMD over a
ing pattern of BMD decrease; we could also think at the
time interval of months, e.g. 50 days. The formula
confounding patterns of IRIS in HAART therapy, co-
obtained is
morbidity of osteopetrosis and osteoporosis, multiple
myelomas, breast cancer, diabetes and metabolic syn- fBD (t + t) − fBD (t)
dromes, etc. The variance could perhaps help in discri- , t = 0, 10, ..., 1200.
t
minating among bone-related diseases. From a technical
viewpoint, properties to verify have been formulated in • Density variance. While the first estimator com-
CSL (Continuous Stochastic Logic) [19], and they give putes the expected value of bone density, here we
rise to three clinical estimators that we evaluate over calculate the variance of BMD taking into account
1200 days (about four years), which is enough to assess the whole state space and the actual bone density at
the presence of bone diseases: each state.
• Bone density estimator. It is calculated as the dif- Figure 6 and Figure 7 describe bone mineral density,
ference between the cumulative (C ≤t ) expected standard deviation and density change rate functions for
rewards (ℛ {”..."} ) for bone formation and bone the control (a), osteoporosis (b) and osteomyelitis (c)
resorption, with the formula cases, respectively. Clearly the osteomyelitis case shows
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Figure 6 Bone mineral density function and its standard deviation for the control (left, a), osteoporosis (middle, b) and osteomyelitis
(right, c) simulations.
quicker decrease than control and osteoporosis cases. methodological point of view the combination of mathe-
They provide an example of how the diagnostic estima- matical and formal method approach has led to the pro-
tors could be derived. Therefore our work is meaningful posal of considering additional estimators (first
in perspective of a clinical bioinformatics characterized derivatives and variance) of the bone pathologies as
by a close coupling between clinical measures and mod- diagnostic tool. That could also inspire the ideal situa-
elling prediction. tion in which a personalised model is generated from
Here we report that the genetic complexity and the (personalised) data and the comparison between clinical
gene expression data meta analysis shows that the data obtained during periodic medical check-up is com-
underlying “mystery” of bone remodelling is much pared with the computer predictions.
greater than handled by the current mathematical mod-
els. In other words we are not able to use all our gene Methods
expression results in a full model of BR diseases. Data analysis
Although our model of osteomyelitis and the compari- We found that there are no comprehensive analysis on
son with the osteoporosis is not able to consider all this osteomyelitis; most studies focus on specific conditions.
complexity, nevertheless it makes a partial use of the We have collected a large ensemble of gene expression
results of the analysis of the experimental data and pro- data related to osteomyelitis and osteoporosis. For this
duces a realistic description of the pathology. From a reason, we have considered 6 microarray data sets of the
Figure 7 Rate of change of bone mineral density function for the control (left, a), osteoporosis (middle, b) and osteomyelitis (right, c)
simulations.
Liò et al. BMC Bioinformatics 2012, 13(Suppl 14):S12 Page 13 of 14
http://www.biomedcentral.com/1471-2105/13/S14/S12
same platform GPL96 from the Gene Expression Omni- non-trivial models, due to the combinatorial explosion
bus (http://www.ncbi.nlm.nih.gov/geo/), accession num- of the state space. For this reason, verification has been
bers are GSE16129, GSE6269, GSE11907, GSE11908, performed by means of approximate probabilistic model
GSE13850 and GSE7429 [20-23]. We observe that checking techniques that calculate the probability of a
RANKL, RANK, OPG and NF-kB proteins impact more given property on a statistical basis, i.e. by sampling on
on the bone remodelling for osteomyelitis and osteo- a number of simulations of the model. In this work we
porosis [7,20-22]. For this reason to understand the have taken 20 samples for each verified property, that
effect osteomyelitis and osteoporosis on bone remodel- were enough to reproduce outputs similar to the non-
ling, we have considered the genes related to the pro- approximate verification. PRISM models could be made
teins RANKL, RANK, OPG, NF-kB proteins, TNF and available upon request to the second author.
TNF receptor superfamilies. We observed that there are
82 genes are related with these proteins. So, we filtered
Acknowledgements
the required 82 genes related data. We have selected We thank Bruce P. Ayati (Iowa University) and Glenn Webb (Vanderbilt
samples for 48 infected and 27 healthy controls for University) for suggestions and help in computation.
osteomyelitis and 30 infected and 30 healthy controls This article has been published as part of BMC Bioinformatics Volume 13
Supplement 14, 2012: Selected articles from Research from the Eleventh
for osteoporosis. The datasets contain data from people International Workshop on Network Tools and Applications in Biology
of different age and sex. (NETTAB 2011). The full contents of the supplement are available online at
For more evidence about osteomyelitis, we have con- http://www.biomedcentral.com/bmcbioinformatics/supplements/13/S14
sidered more gene expression data related to osteomye- Author details
litis on different platform GPL97. For this reason, we 1
Computer Laboratory, Cambridge University, William Gates Building, 15 JJ
have considered additional 3 microarray data sets from Thomson Avenue, Cambridge CB3 0FD, UK. 2School of Science and
Technology, Computer Science Division, University of Camerino, Via
the Gene Expression Omnibus (http://www.ncbi.nlm. Madonna delle Carceri 9, Camerino (MC) 62019, Italy. 3Department of
nih.gov/geo/), accession numbers are GSE6269, Mechanical Engineering, University of Sheffield, Sir Frederick Mappin
GSE11907 and GSE11908 [21,22]. To understand the Building, Mappin Street, Sheffield S1 3JD, UK.
effect of osteomyelitis on the bone remodelling, we have Authors’ contributions
considered the genes related to the proteins RANKL, LP and NP conceived and designed the models, MM carried out data
RANK, OPG, NF-kB proteins, TNF and TNF receptor analysis. All authors contributed writing, reading and approving the final
manuscript.
superfamilies like previous analysis. We observed that in
the platform GPL97, there are 31 genes are related to Competing interests
these proteins and superfamilies. So, we filtered the The authors declare that they have no competing interests.
required genes related data. We have selected samples Published: 7 September 2012
for 43 infected and 17 healthy controls. Standard anova
and Box plots representation were used to analyse and References
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Liò et al. BMC Bioinformatics 2012, 13(Suppl 14):S12 Page 14 of 14
http://www.biomedcentral.com/1471-2105/13/S14/S12
doi:10.1186/1471-2105-13-S14-S12
Cite this article as: Liò et al.: Modelling osteomyelitis. BMC Bioinformatics
2012 13(Suppl 14):S12.