review open access a multiscale systems perspective on ... · a multiscale systems perspective on...

REVIEW Open Access

A multiscale systems perspective on cancerimmunotherapy and Interleukin-12David J Klinke II12

Abstract

Monoclonal antibodies represent some of the most promising molecular targeted immunotherapies Howeverunderstanding mechanisms by which tumors evade elimination by the immune system of the host presents asignificant challenge for developing effective cancer immunotherapies The interaction of cancer cells with the hostis a complex process that is distributed across a variety of time and length scales The time scales range from thedynamics of protein refolding (ie microseconds) to the dynamics of disease progression (ie years) The lengthscales span the farthest reaches of the human body (ie meters) down to the range of molecular interactions (ienanometers) Limited ranges of time and length scales are used experimentally to observe and quantify changes inphysiology due to cancer Translating knowledge obtained from the limited scales observed experimentally to pre-dict patient response is an essential prerequisite for the rational design of cancer immunotherapies that improveclinical outcomes In studying multiscale systems engineers use systems analysis and design to identify importantcomponents in a complex system and to test conceptual understanding of the integrated system behavior usingsimulation The objective of this review is to summarize interactions between the tumor and cell-mediated immu-nity from a multiscale perspective Interleukin-12 and its role in coordinating antibody-dependent cell-mediatedcytotoxicity is used illustrate the different time and length scale that underpin cancer immunoediting An underly-ing theme in this review is the potential role that simulation can play in translating knowledge across scales

IntroductionTherapies targeting particular molecules relevant in thepathogenesis of cancer promise efficacy in stratifiedpatient groups with minimal side effects Breast cancer is aprime example where a molecular therapy - trastuzumab -has been shown to have remarkable efficacy in patientswith tumors that overexpress one of the epidermal growthfactor (EGF) receptors ErbB2 [12] In 25-30 of breastcancer patients the ErbB2 receptor is overexpressed and iscorrelated with a poor prognosis [3] Trastuzumab is amonoclonal antibody that specifically targets the ErbB2receptor and blocks the interaction of ErbB2 with othermembers of the EGF receptor family [45] Trastuzumabhalts abnormal cell proliferation by decreasing ErbB2expression through sequestering it in endocytic vesiclesresulting in receptor degradation [6] Yet one of the per-sistent challenges in cancer research is understanding whypatients who overexpress these targeted proteins either do

not respond at all or ultimately become resistant to thetherapy For instance only 12-34 of patients that overex-press ErbB2 respond to trastuzumab by itself and thenonly for a mean period of 9 months [17] The fact that allpatients eventually develop resistance to trastuzumabrepresents an important and poorly understood clinicalproblem (eg [89]) Moreover monoclonal antibodiesform one of the largest classes of molecular targeted thera-pies for cancer [10] While molecular targeted drugs attacka single target it is increasingly evident that a multitude offactors (eg immunological bias genetic predispositionand oncogenic changes) contributes to cancer etiologyUsing the immune system as a source of patient-generatedantibodies to provide a similarly selective but also adaptivetherapy has intrigued immunologists and cancer biologistsfor decades [11] In the recent decade the concept of can-cer immunoediting holds renewed promise followingnumerous studies on human immunodeficiencies that pro-vide support for the role of lymphocytes (eg T NK andNKT cells) and cytokines in regulating primary tumordevelopment [12] Adjuvants such as Interleukin-12 also

Correspondence davidklinkemailwvuedu1Department of Chemical Engineering and Mary Babb Randolph CancerCenter West Virginia University Morgantown WV 26506-6102 USAFull list of author information is available at the end of the article

Klinke Molecular Cancer 2010 9242httpwwwmolecular-cancercomcontent91242

copy 2010 Klinke licensee BioMed Central Ltd This is an Open Access article distributed under the terms of the Creative CommonsAttribution License (httpcreativecommonsorglicensesby20) which permits unrestricted use distribution and reproduction inany medium provided the original work is properly cited

hold promise for augmenting antitumor immunotherapy[13]Interleukin-12 (IL-12) is an important immune regu-

latory cytokine that exerts potent antitumor activityand a member of a small family of heterodimeric cyto-kines [1415] In the literature IL12 implicitly refers toa 75-kDa heterodimer that is formed by the disulfide-linkage of two independently regulated gene productsa 40 kDa (p40) subunit and a 35 kDa (p35) subunit[16] The p40 subunit as a homodimer (IL12(p40)2) ormonomer (IL12p40) can also bind to the IL-12 recep-tor resulting in interactions that antagonize IL12p70binding both in mice [1718] and humans [19] Thebioactivity of IL-12 is due to the competitive bindingof all isoforms with the IL-12 receptor [20] In the per-ipheral tissues IL-12 originally called Natural KillerCell Stimulating Factor enhances the ability of NKcells to lyse target cells a mechanism exploited fortumor immunotherapy [21] As an adjuvant IL-12 pro-motes NK-cell mediated killing of HER2-positivetumor cells in patients treated with trastuzumab[22-24] Yet despite the sincere efforts of many tounderstand the complicated relationship between can-cer and the immune system translating the therapeuticpotential of immunotherapies observed in vitro and inanimal models to the clinic has been difficult [25]One of potential sources for this difficulty has been

how we have predominantly approached this problemldquoDivide and conquerrdquo has been used to describe the pre-dominant mode of scientific inquiry in the medicalsciences [26] The underlying assumption is that under-standing the behavior of a complicated system can beachieved by deconstructing the system into more funda-mental components and characterizing the behavior ofthe components In studying the fundamental compo-nents in isolation we may miss collective interactionsthat are important for understanding how the integratedsystem works In addition this reductionist approachtowards scientific inquiry also spawned subdisciplinesthat focus on specific aspects of biological systems Forinstance the study of protein structure and folding typi-cally falls under the purview of biophysics the study ofmetabolic and signaling pathways falls under the purviewof biochemistry and the study of emergent behavior ofpopulations of immune cells to biochemical cues fallsunder the purview of immunology The engineering dis-ciplines have taken a different approach towards under-standing natural and synthetic systems For instancechemical engineering has a rich history where theory andmathematics provide a framework for analyzing design-ing and controlling reacting systems [2728] One of theunifying concepts in the discipline is that theory andmathematics can be extended using simulation Usingsimulation engineers predict the behavior of complicated

systems using knowledge of system components and the-ories (eg transport phenomena and chemical kinetics)that describe how we expect the components to interactThese predictions are then tested experimentally to askthe question is our incomplete knowledge of the systemcomponents sufficient to reconstruct the behavior of thesystem In the process a more fundamental question isasked is this system complicated (ie components inter-act via defined rules that we can characterize in isolation)or is it complex (ie the behavior of components is anemergent behavior that can only be characterized bystudying the integrated system) Collectively this processis a knowledge generating activity [29] This process alsohelps manage uncertainty do we understand the systemsufficiently to make a decision or do we need to gathermore data From this perspective research activities asso-ciated with the disciplines of engineering and basic medi-cal sciences represent contrasting modes for acquiringknowledge about systems (ie reconstruction versusdeconstruction) The objective of this review is todescribe methods used in engineering to study systemsand to analyze cancer immunotherapy from an engineer-ing perspective using IL-12 as an illustrative example

Systems Analysis and Identifying ScalesWhen presented with a complex problem such as devel-oping a novel immunotherapy a common problem-solving approach is to first identify the importantcomponents whose interactions define system behaviorAdvances in molecular biology during the twentiethcentury provided experimental tools to identify the indi-vidual components of complex biological systems [30]Once identified the function of these components andtheir interactions can be characterized In engineeringthis process is called systems analysis [31]Knowledge obtained by systems analysis is coupled to

the experimental techniques that scientists use to probesystems and the computational tools that are used tointerpret those experimental observations One of theparticular techniques used in systems analysis is to iden-tify the different time scales that underpin the responseof a dynamic system (ie a time scale analysis) to anabrupt change in environmental conditions A timescale analysis aids in simplifying the response of asystem by parsing system components and their corre-sponding dynamics into different kinetic manifolds (eg[32]) The evolution in the system is constrained by theslow variables (ie the slow kinetic manifold) while thefast variables (ie the fast kinetic manifold) exist at apseudo-equilibrium Moreover variables that exhibittime scales significantly longer than the time scale overwhich the system has been observed can be consideredstationary (ie a stationary manifold) This phenomenonrelated to separating time scales has been termed the


Page 2 of 18

slaving principle [33] From observed differences in timescales we can infer that the important components thatregulate the system dynamics correspond to the slowkinetic manifold Components that correspond to a sta-tionary manifold do not need to be represented expli-citly as their contributions can be lumped intoappropriate rate parameters Components that corre-spond to a fast kinetic manifold can be described usingequilibrium relationships (ie experimentally measurableequilibrium dissociation constants rather than kineticrate parameters) Time scale analysis is a classical tech-nique used to identify key enzymes that control fluxwithin [34] and quantify hierarchical relationshipsamong elements of a complex metabolic network [35]Similarly the distance over which components interact

(ie a characteristic length scale) can also be identifiedIn systems where components move (ie diffuse) andcan be transformed (eg degradation of a protein ligandupon binding to a cell) a characteristic length scale canbe defined as a ratio between the rate parameters fordiffusion and reaction [36] This approach has beenused to explain the inverse relationship between pene-tration of therapeutic antibodies into tumor spheroidsand the affinity of the antibody to the tumor antigencalled the ldquobinding site barrierrdquo [37] The effective depthof penetration l is defined as

=[ ][ ]

D Abk Ag

sdotsdot

o

e o(1)

where D is the effective diffusion coefficient for antibodypenetration into tumor spheroids [Ab]o is the concentra-tion of antibody in the tissue ke is the rate constant forthe catabolism of antibody upon binding to the corre-sponding tumor antigen as represented by the averageconcentration of the tumor antigen within the tumor ([Ag]o) [38] Note that the length scale in this example l is afunction of the rate parameter ke The rate parameters arealso used to estimate time scales This highlights the directrelationship between time and length scalesCancer is a complex multiscale system that spans mul-

tiple time (eg milliseconds to years) and length scales(eg nanometers to meters) [39] In studying cancer weimplicitly focus on a narrower range of scales to askmore focused questions how do immune cells processinformation at the molecular level how does the immunesystem shape tumor cell populations or are there geneticdifferences associated with clinical response to a cancerimmunotherapy This implicit partitioning of a multiscalesystem into a series of subsystems that are constrained toa narrower range of time and length scales aids in redu-cing the complexity of the problem A set of subsystemsthat are relevant to cancer immunotherapy include thepeptide protein cell organ and patient levels as

depicted in Figure 1 Given the direct relationshipbetween time and length scales the subsystems areplaced along the diagonal in this diagram The labels cor-respond to the basic component unit within each of sub-system Within each of these subsystems knowledgeregarding the behavior of components within a particularsubsystem is inferred from observed data and prior infor-mation Following from the ldquoslaving principlerdquo informa-tion passes from subsystems that exhibit shorter timeand length scales to subsystems that exhibit longer timeand length scales This can be represented as the traffick-ing of information from the bottom upwards as high-lighted by the blue arrows in Figure 1 For instance thedynamic distribution in conformational states at the pep-tide level is summarized in terms of a protein-proteininteraction energy (ie protein activity) The activity of aprotein provides prior information for higher time andlength scales Absent any alterations in protein structure(eg SNPs or mutations) the energetics of protein-pro-tein interactions that contribute to the existence of edgeswithin a canonical signaling network are typicallyassumed to be conserved across systems How a cell pro-cesses information via a signaling network is then deter-mined from observed measurements in changes inexpression or activity of an intermediate signaling pro-tein given known protein-protein interactions In model-ing cell level behavior it may not be necessary toincorporate details regarding the dynamics of a signalingnetwork nor to incorporate protein-folding dynamics Itmay be sufficient to represent signaling networks as acollection of rules that relate extracellular signal to cellu-lar response (ie an integrated cellular response surface)These rules may represent simple input - simple outputrelationships (ie how a change in a single cytokine influ-ences cellular proliferation) or they may represent multi-ple input - multiple output relationships to account forcontext-dependent behavior (ie how changes in multi-ple cytokines collectively influence cellular survival andcytokine production) In the following sections wewill expand on this multiscale concept by focusing onInterleukin-12 and its role in coordinating antibody-dependent cell-mediated cytotoxicity

The Peptide LevelCellular response to extracellular stimuli is governedby protein-protein interactions that allow the transferof information from the cell membrane to the nucleusand back [40] Proteins interact through functionalmotifs that characterize the affinity and specificity fora particular motif-motif interaction [41] Within thismultiscale hierarchy the peptide level focuses on iden-tifying changes in the protein structure that redistri-bute the energetic states of a system to preferdifferent conformations [42] When two proteins


Page 3 of 18

interact via motifs the distribution in energetic statesof the protein complex reaches an equilibrium distri-bution within seconds and may propagate beyond themotif-motif interaction region The equilibrium distri-bution in states characterizes the affinity for a particu-lar protein-protein interaction Somatic mutations orgermline single-nucleotide polymorphisms in the cod-ing region of genes alter the primary protein structureresulting in a different affinity for protein-proteininteractions that contain the mutated protein (eg[43]) Experimentally the binding affinity for motif-motif interactions can be measured using high-throughput in vitro methods [4445] The energeticsfor motif-motif interactions measured in vitro may notcorrespond to the actual binding affinities of two

proteins within a cell that interact through a particularmotif pair Macromolecular crowding or other struc-tural aspects of the proteins may influence the abso-lute value of the binding affinity However the relativedifferences among the different motif-motif interac-tions do predict which proteins become activatedupon direct interaction with receptor tyrosine kinases[46] Alternatively the distribution in energetic statesof a protein can be obtained using simulation as sum-marized by [47] Simulation or high-throughputexperimental methods can both be used to identifyhow alterations in the amino acid sequence alter thestructure of a protein Thus the objective of this levelwould be to infer protein-protein interaction strengthbased upon data that describes changes in genotype

100

102

104

106

108

1010

10-8

10-6

10-4

10-2

100

102

Time scale (sec)

Leng

th S

cale

(m)

Peptide

Protein

Cell

Patient

Peptid

Dynamic Intercellular In VitroAssays

DynamicIntracellular In VitroAssays

Dynamic In VivoStudies

ClinicalStudies

SNPsGenotype

Data

InferenceD I

D I

D I

D I

CollapseDynamicCellular

Heterogeneity

Predict Prototypic Cell

PopulationResponse

Predict Integrated Cellular Response Surface

CollapseDynamic

Variation in Protein Activity

Predict ProteinActivity

CollapseVariation in

Folding States

IL-2

Dendritic Cells

Naiumlve CD4+

T Cells IL-4

IL-12IFN-

Th2

Th1

IL-2IFN-

IL-4IL-5IL-10IL-13

IL-23IL-17

Th17

IL-2

TDendritic Cells

Naiumlve CD4+

T Cells IL-4

IL-12IFN-

Th2Th2

Th1Th1

IL-2IFN-

IL-4IL-5IL-10IL-13

IL-23IL-17

Th17

Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode

Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode Circulatory

System

LymphNode

Carcinoma

StromaNK Cell

CirculatorySystem

LymphNode

Carcinoma

StromaNK Cell

Oncogenesis

Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode

eeeeeeeeeeeStromaS Fibroblasts

CCC

eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeStroStromaStromaStromaStroma FibroblastsFibroblastsFibroblastsFibroblasts

CCCCCCCCCCCCCSSSSSSSSSSSSSSSSSSSSS

a

CC ryCCmphLymphhL hdNodeedddN d

OnOnOnOnnnOnOnnOnnOncococococoooocooooooococoooocooooooocooooooooooooooooooooooooooooooooooooooooooooooooooooooocooooooooooocooooooooooooooooooooooooooooooooooooggegegggggegegegegggegeggggggegegegegegegegegegeggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggomaomaomaoma FibroblastsFibroblastsFibroblastsFibroblastsFibroblasts

CirculatoCirculatoCirculatolatoi ryryyryrrCirculatoirculatoCirculatolatoi ryryryrrCirculatoirculatoCirculatolatoi ryryryrrCirculatoirculatoCirculatolatoi ryryryrrLymphmphLymphmphmppmphLymphmphmppmphLymphmphmppmphLymphmphmpp

dedNodedeededeNodedeeddedNodedeedddedNodedeededNodedeedystemSystemmmmmyySystemSystemSystemSystemstemystemteSystemystemSystemSystemmeSystemystemSystemSystememeSystemystemSystemSystemme

Epithelium

Stroma Fibroblasts

CirculatorySystem


System

LymphNode

Carcinoma

StromaNK Cell

CCCCCCCCCCCCSSSSSSSSSSSSSCirculatoCirculatoCirculatoculatoatoirculatu ryryyryryCirculatoirculatoCirculatoulatoatoircula ryryyryryCirculatoirculatoCirculatoulatoatoircula ryryyryryCirculatoirculatoCirculatoulatoatoircula ryryyryrySystemSystemSystemmSystemSystemySystemSystemSystemmSystemSystemySystemSystemSystemmSystemSystemySystemSystemSystemmSystemSystemy

LymphmphmphLymphmphmpLymphmphmpLymphmphmpNodedeeeeNodedeeeeNodedeeeeNodedeeee

ee

CarcinomaCarcinomaCarcinomaCarcinoma

StromaStromaStromaStromaNK NKNKNKNKCellCell

enennnnnnnnnnnnnnnnnnnnnnnnnnn sissssssssssssssssssssssssssssss sssssseeeeeeesisisisisssssssssssssssssssssssssssssssss ssssssCirculatorySystem

LymphNode

Carcinoma

StromaNK Cell

Oncogenesis

Organ

lt

Leng

th S

cale

(m)

Time Scale (sec)Figure 1 An overview of the multiple time and length scales involved with understanding cancer immunotherapy Five subsystems areshown that each represent a limited range of time and length scales and are named after the basic functional unit peptide protein cell organand patient Within each subsystem knowledge about behavior of a particular subsystem is inferred from observed data as depicted by the redarrows and prior information as depicted by the blue arrows that enter each subsystem box Each experimental assay has an intrinsic lengthand time scale and thus inform the corresponding subsystem Prior information for interpreting data within a subsystem can be obtained from asummary of the dynamics of subsystem with shorter time and length scales This summary of the dynamics may take the form of equilibriumvalues or population-based averages


Page 4 of 18

A series of genome association analyses have identifiedpolymorphisms associated with proteins involved in theIL-12 signaling axis These polymorphisms are typicallyidentified as they correlate with different phenotypeswithin a clinical population The phenotypes may bedirectly (eg oncogenic) or indirectly (eg alter tumorimmunosurveillance) related to cancer In particulargenetic mutations in IL-12p40 and one component of theIL-12 receptor IL-12Rb1 have been observed in patientswith recurrent mycobacterial disease [4849] Heterozygousmutations in the other component of the IL-12 receptorIL-12Rb2 have been reported in atopic patients that corre-late with a reduction in STAT4 phosphorylation the cen-tral transcription factor in the IL-12 pathway and IFN-gproduction in response to IL-12 stimulation [5051] A sin-gle point mutation (Val617Phe) in the JAK2 a JanusKinase that forms a complex with IL-12Rb2 associateswith myeloproliferative disorders [52] promotes the con-stitutive activation of the kinase and enables the enzymeto escape negative regulation by SOCS3 [53] In contrastmutations that impair kinase activity in TYK2 a memberof the Janus Kinase family that interacts with IL-12Rb1have been associated with reduced IL-12 responsiveness[54] Association of coding single nucleotide polymorph-isms (SNPs) within the Tyk2 gene with disease in humanshas also been identified [5556] A reduced response toIL-12 similar to an increase in atopy and susceptibility tomycobacterial disease is an indication for reduced cell-mediated cytotoxicity an important effector mechanismfor tumor immunosurveillance In principle an under-standing of how genotype influences protein-protein inter-action strength provides prior information for the nextlevel the Protein level However the structural implica-tions of many of these mutations remain unclear Identify-ing the physiological implications of SNPs is also difficultdue to the overlapping roles that the intracellular signalingproteins play in other signaling pathways For instanceTYK2 plays a role in IFN-a [57] and IL-23 [58] signalingin addition to IL-12 signaling Longer time and lengthscales provide additional perspectives for addressing thesequestions

The Protein LevelThe next larger time and length scale focuses on interac-tions between proteins that occur within the cell Thecollective protein-protein interactions form networkssuch as metabolic and signaling networks The structure(ie topology) of these networks is described by a seriesof nodes and edges The nodes are the individual proteinsand the edges in the case of signaling networks corre-spond to the velocity of information flow due to protein-protein interactions The topology of signaling networksmay be inferred from in vitro assays that measurechanges in the intracellular state of signaling proteins in

response to a suite of stimuli using Bayesian computa-tional methods [59] Alternatively canonical pathwaysare proposed that summarize the collective scientificevidence in support of the topology of a particular signal-ing network (eg [60] and the KEGG PATHWAY data-base httpwwwgenomejpkeggpathwayhtml) In theliterature these networks are frequently represented asqualitative cartoons that illustrate simple linear ldquobucketbrigadesrdquo where information is passed from one proteinto another [61] However cellular signaling networkshave evolved to have complex characteristics includingredundancy (whereby signals are dispersed among multi-ple pathways) and complex feedback loops (wherebysignals are amplified or dampened as they pass through aparticular pathway) [62] As an illustrative example ofthis complexity consider the IL-12 signaling networkCellular response to IL-12 occurs via one member of

the canonical Janus kinase (JAK) and signal transducerand activator of transcription (STAT) family of signalingpathways [63] Signal transduction originates with theIL-12 receptor a member of the type 1 cytokine recep-tor family and comprised of two subunits IL-12Rb1 andIL-12Rb2 These receptor subunits lack intrinsic enzy-matic activity and require association with specific Januskinases JAK2 and TYK2 to transmit cellular signalsBinding of a natural ligand to an IL-12 receptor precipi-tates a series of biochemical events the receptorchanges conformation the tyrosine residues on thereceptor become phosphorylated by receptor-associatedJanus kinases signaling proteins associate with the acti-vated receptor (eg STAT4) and the signaling proteinsin turn become phosphorylated In the IL-12 signalingnetwork phosphorylated STAT4 translocates to thenucleus to promote the transcription of various responsegenes A subset of these signaling pathways that lead todifferent cellular behaviors is depicted in Figure 2While the canonical JAK-STAT pathway seems rela-

tively straightforward various positive and negative regu-latory pathways modulate the strength and duration ofsignaling As effective signaling via the IL-12 pathwayrequires the expression of IL-12Rb2 phosphorylatedSTAT4 promotes the upregulation of the IL-12Rb2 subu-nit [64-66] creating a positive feedback loop A predomi-nant pathway for negative feedback regulation of IL-12signaling is via the family of Suppressor of CytokineSignaling (SOCS) Specifically SOCS1 inhibits IL-12signaling [6768] and SOCS3 negatively regulates IL-12signaling by blocking the binding of STAT4 to theIL-12Rb2 subunit [69] Message for both SOCS1 andSOCS3 increases in IL-12-stimulated peripheral bloodT cells [70] However the mechanism by which SOCSproteins regulate cytokine-receptor signaling remainsunresolved [63] The current model for SOCS regulationof the JAKSTAT signaling is that the E3 activity of the


Page 5 of 18

SOCS protein targets the substrate for ubiquitination andsubsequent proteosomal degradation [71] In contrastgenetic studies suggest that the SH2 domain of the SOCSprotein blocks cytokine-receptor signaling by itself [69]In addition the protein inhibitors of activated STATs(PIAS) (aka SUMO) are also negative regulators ofcytokine signaling [7273] In particular PIAS inhibits IL-12 signaling by sequestering STAT4 and thereby inhibit-ing STAT4-dependent gene transcription [74]As illustrated by the IL-12 signaling example many of

the molecular players in the various signaling pathwaysare known However the regulatory roles that individualproteins play at specific points in time and in particularsystems are largely unknown [75] It is precisely in this

situation that mathematical models are most helpful [39]These models are typically based upon theories that areused to describe how proteins interact For example thetransfer of information within intracellular signaling net-works has been described in terms of a cascade of activat-ing (eg kinase action) and deactivating (eg phosphataseaction) events that modify intermediate signaling proteins[76] (see Figure 3) Within a level of this cascade thesteady state activation of a signaling protein (A) isdescribed by

AS RS

kd Dka

RS =

2 1

1

sdotsdot +

(2)

p40 p35

BOX1 BOX1

BOX2

811

804

757

TYK2 JAK2

IL12Rβ2IL12Rβ1

PP

STAT4P

SOCS

SOCS PTP

PIAS

N-PTP

Target GenesbullRegulate growthsignaling

bullPromote differentiation

STAT4

STAT4P P

STAT4

STAT4P P

STAT4

STAT4

STAT4

STAT4

Cofactors

+

ExtracellularEnvironment

Cytosol

Nucleus

IL12Rβ2

Figure 2 A schematic diagram of the flow of information from the extracellular environment to the expression of target genes in thenucleus by the canonical IL-12 signaling network These signaling networks originate at the cell membrane following the activation ofdimers of the cytokine receptors such as IL12Rb1-IL12Rb2 The yellow bars on the IL12Rb1 and IL12Rb2 receptors indicate the particular tyrosineresidues within the intracellular portions of the receptors In the mouse STAT4 interacts primarily with the tyrosine residues Y757 Y804 and Y811on IL-12Rb2 The green bars indicate the BOX motifs that interact with the kinases TYK2 and JAK2 The orange boxes correspond to canonicalJanus Kinases TYK2 and JAK2 that interact with the IL-12 receptor Key signaling proteins within individual pathways are shown The red linesindicate protein-protein interactions that negatively regulate this signaling network


Page 6 of 18

where S2 is the total concentration of signaling pro-tein in both active (A) and inactive (I ) conformationsRS1 is the concentration of activating protein complexD is the concentration of deactivating protein and kaand kd are the rate constants associated with activatingand deactivating proteins respectively [77]Cellular response is proportional to the abundance of

A While changes in peptide structure alter the rate con-stants changes in abundance of any of the participatingproteins (eg RS1 S2 and D in Equation 2) can alsoinfluence cellular response to a particular biochemicalcue These changes in protein expression within a cellare assumed to occur quicker than changes in cell popu-lations and therefore limit the range of relevant time-scales Research questions at the protein level focus ontwo aspects 1) how genetic variation influences the flowof information within a signaling pathway and 2) how

proteins are dynamically regulated to shape cellularresponse In the following paragraphs each of theseaspects will be discussed separatelyAs suggested by the theory encoded in equation 2

changes in the expression of proteins involved in theIL-12 signaling network will alter the cellular responseto IL-12 Similar to coding polymorphisms described inthe Peptide section polymorphisms in untranslatedregions of proteins involved in the IL-12 signaling axishave been identified in genome association studiesAlterations in the genome in untranslated regions canaffect the expression of genes and their correspondingproteins For instance a recently discovered mechanismfor posttranscriptional regulation of gene expression isvia miRNAs [78]Untranslated regions (UTR) of mRNA provide binding

sites for regulatory miRNAs Shortened 3rsquoUTRs are asso-ciated with oncogenic transformation in cancer cell linesa loss of miRNA target sites and an increase in expres-sion of the corresponding proteins [79] While no poly-morphisms have been identified yet miRNA have beenassociated with the IL-12 signaling network includingmiR-21 that regulates mIL-12p35 expression [80] miR-135a that regulates JAK2 expression [81] and miR-155that regulates SOCS1 expression [82] These miRNA mayrepresent regulatory components of a signaling-depen-dent translational control structure that influences theflow of information within the IL-12 pathway While notspecifically associated with miRNAs a polymorphism inthe 3rsquoUTR of the IL-12p40 gene has been associated witha reduction in plasma IL-12p40 [8384] and an increaserisk for carcinoma [8586] lymphoma [83] and glioma[84] In the 5rsquo regions single nucleotide polymorphismsin the 5rsquo flanking region of the IL-12Rb2 gene is asso-ciated with aggressive periodontitis [87] In additionSNPs in the non-coding regions of the STAT4 [88] andIL-12Rb2 [89] genes have been associated with anincreased risk for autoimmunity SNPs in the non-codingregions of Tyk2 associate with increased risk for inflam-matory bowel disease [90]Besides single-nucleotide polymorphisms other

genetic and epigenetic changes modulate protein expres-sion Chromosomal translocations may switch the corre-sponding promoter to a more active one or change theregulation of gene expression [91] Structural genomicvariation with the majority smaller than 10 kb is amajor contributor to phenotypic variation within thenormal human genome [9293] The highest proportionof genes affected by the identified variants modulatescellular response to extracellular signals (eg receptorsignaling networks) One of the functional effects ofstructural genomic variants is a change in the level ofexpression of gene products for a given transcriptionsignal Alterations in DNA copy number variants have

Biochemical Cue(eg IL-12)

Signaling Protein 1

(S1)

RS1Complex

Receptor(R)

InactiveSignaling Protein 2

(I)

ActiveSignaling Protein 2

(A)

Cellular Response (CR)(eg Cytokine

Production)

DeactivatingProtein (D)

Cue-Signal-Response Model

ka

kd

Figure 3 A conceptual model of the flow of information withinan intracellular signaling network Biochemical cues initiate acellular response by interacting with receptors Cellular receptorsmodify intermediate signaling proteins via a cascade of activatingand deactivating events Changes in activity of these intermediatesignaling proteins ultimately regulate cellular response In this twolevel cascade an activated receptor (R) interacts with signalingprotein 1 (S1) to form a multi-protein complex (RS1) The activity ofsignaling protein 2 is determined by the balance betweenactivation and deactivation rates The activation and deactivationrates are related to the abundance of the RS1 and deactivatingprotein (D) respectively Cellular response is proportional to theactivity of signaling protein 2


Page 7 of 18

also been observed in solid tumors [94] Epigeneticmechanisms also regulate gene expression and promoteoncogenesis [95] Epigenetic silencing of the IL-12Rb2gene via DNA methylation has been observed in chronicB-cell malignancies compared to normal B-cells [96]and primary lung adenocarcinomas [97]The theory encoded in equation 2 can be extended

using mathematical models To create a mathematicalmodel one must first specify the causal relationshipsamong the interacting proteins involved in a signalingnetwork (ie the network topology) Similar to Bayesiannetworks ordinary differential equation (ODE)-basedmathematical models provide a computational frame-work for expressing the current knowledge regarding thetopology of a signaling network Historically the topol-ogy of a reaction network has been assembled manuallythrough the judicious use of simplifying assumptions(eg [98-100]) These manually assembled networks haveprovided insight into many signaling pathways [62]However the implicit assumptions required for manualassembly of reaction networks impose bias and limitwider application [101] One of the advances in the fieldof reaction pathway analysis has been the creation ofalgorithms that automatically generate reaction networksusing formalized descriptions of molecular transforma-tions [102103] Algorithms that automate model con-struction allow the researcher to focus on interpretingthe biochemistry described by the model rather than onits tedious assemblyGraph theory is a useful mathematical framework that

facilitates constructing a reaction network among react-ing species [104] and provides the fundamental basis forthese algorithms The generality of the approach lendsitself to representing different reacting systems withminimal modification to the algorithm Examples ofapplications include reaction networks that containhydrocarbons [105] immobilized binding sites [106]and multi-state proteins [107-111] Representing multi-state proteins as a collection of functional motifs [41] isa key concept that enables applying this computationalapproach to signaling networks Reaction networks likecell signaling networks can be constructed based uponthe systematic application of ldquorulesrdquo that provide con-straints on the formation and destruction of motif-motifldquobondsrdquoApplication of the rules to reacting species can create

reaction networks that exhibit combinatorial complexity[112] leading to a combinatorial explosion in the numberof unique species represented in the model [111] How-ever computational tools have been developed to prunethe reaction network based upon specific criteria and tofacilitate intuitive interpretation of model behavior[105113] Once the network topology has been specifiedODE-based models provide quantitative predictions

following the specification of initial conditions for themodel variables and of values for the reaction parametersInitial conditions can be estimated from protein expres-sion measurements and reaction parameters can be esti-mated using protein-protein affinity data dynamiccalibration data and thermodynamic constraints (see[114] as an example)Unlike Bayesian networks ODE-based models can be

used to infer how proteins dynamically regulate the flowof information down different branches with a signalingnetwork from observed data [115] However the abilityof a particular mathematical model to describe a systemof interest analogous to experimental studies mustinclude a statement of belief Belief derived from amathematical model is expressed commonly in terms ofa single point estimate for the predictions obtainedfrom the set of parameters that minimizes the variancebetween model and data [116] Given that a model con-strains the set of possible states of the system it isessential to provide an estimate of the uncertainty asso-ciated with the model predictions given the availabledata The use of single point estimates is a frequentpoint of contention in the use of mathematical modelsas the values for many of the parameters are not pre-cisely known The logical argument is that if the uncer-tainty in values of the model parameters is high thenthe uncertainty in the model predictions should also behigh However recent developments in methods forBayesian model-based inference address this concernA Bayesian view of statistics is a mathematical expres-

sion of our beliefs [117] Beliefs are established basedupon the observation of data and the interpretation ofthat data within the context of our prior knowledge[118] Mathematical models provide a quantitative frame-work for representing prior knowledge of the detailedbiochemical interactions that comprise a signaling net-work The unknown parameters of the model are cali-brated against the observed network dynamics Given thecalibration data and the postulated model the uncer-tainty in the model predictions can be obtained using anempirical Bayesian approach for model-based inference[115119] In essence these methods are computationallyintensive methods that randomly walk within parameterspace (ie a Monte Carlo approach) New steps in para-meter space extend the walk A potential new step isevaluated by comparing the model predictions obtainedusing the parameter values of the new step against theavailable data The model predictions for the new stepare only compared against the current step in the ran-dom walk (ie it is a Markov Chain) The similaritybetween the model predictions and the available datacorrespond to the likelihood for including the potentialnew step in the on-going walk High agreement betweenmodel predictions and the available data has a high


Page 8 of 18

likelihood for inclusion in the on-going walk while lowagreement has a low likelihood for inclusion When therandom walk has sufficiently traversed the parameterspace as to provide consistent model predictions theMarkov chain is considered to be converged The collec-tion of model predictions contained within the convergedsegment of the Markov chain provide an estimate of theuncertainty in the model predictions that reflects boththe specific data at hand and the uncertainty in the valuesof model parameters This approach has been used toinfer the strength of different positive- and negative-feed-back mechanisms within the IL-12 signaling network innaiumlve CD4+ T cells obtained from Balbc mice [120]One of the conclusions of this work is that not all of theparameters need to be precisely defined for the model toprovide narrowly distributed predictions In other wordswe can be highly confident in our ability to discriminateamong competing hypothesis regarding the flow of cellu-lar information as encoded in a mathematical modeldespite the underlying uncertainty in the model para-meters Ultimately understanding the dynamic regulationof signaling networks will enable one to map biochemicalcues onto cellular response in the form of deterministiccellular rules This mapping of biochemical cues to cellu-lar response provides prior information for the next levelthe Cell level

The Cell LevelAt the cell level IL-12 is a paracrine cytokine that pro-vides a critical interface between innate and adaptiveimmunity [15] The time associated with an evolvingcell population within a particular organ (eg antigen-induced expansion and polarization of naiumlve CD4+T cells) and the spatial range of paracrine action pro-vide the time and length scale context for this level As

summarized by Figure 4 IL-12 plays a critical rolewithin secondary lymphoid organs in promoting anti-tumor immunity Sufficient and sustained signaling[70] by IL12p70 through the IL-12 signaling networkleads to polarization of naiumlve CD4+ T cells into a Th1phenotype [121] Polarization into a Th1 phenotypepromotes anti-tumor immunity via cytokine help forCD8+ T cell expansion and switching B cell antibodyproduction to isotypes such as IgG2a in the mousethat enhance antibody-dependent NK cell-mediatedcytotoxicity [122]Mature dendritic cells (DCs) are some of the most

prolific producers of IL-12 and play a critical role inregulating the immune response [123124] Anothermember of the IL-12 family IL-23 has been associatedwith promoting polarization towards and expansion of aTh17 subset [125126] and is produced by DCs[127128] However the role of Th17 cells in shapinganti-tumor immunity is still unclear [129] Another reg-ulatory cytokine IL-4 promotes polarization towards aTh2 phenotype [130] In general it is thought that aTh2 bias correlates with tumor tolerance (eg [131])The association of different regulatory cytokines withdifferent T helper cell subsets as illustrated in Figure 4summarizes cell level events that regulate T helper cellpolarization in the secondary lymphoid organs How-ever biochemical cues play different roles in differentorgans due to direct action of biochemical cues on thecells that traffic to specific organs In contrast to its roleas a regulatory cytokine in T helper cell polarizationIL-12 enhances the ability of NK cells to lyse antibody-coated target cells in the peripheral tissues [24] Thisdual role as activator of NK cells and as promoter ofTh1 polarization motivates using IL-12 as an adjuvantfor antibody-based tumor immunotherapy [23]

IL-2

ldquoEducatedrdquoDendritic Cells

NaiumlveCD4+T Cells IL-4

IL-12IFN-γ

Th2

Th1

IFN-γ

IL-4IL-5IL-13

IL-23 IL-17IL-21IL-22Th17

Effe

ctor

CD

4+ T

cel

ls

TGFβ IL-6

Figure 4 An overview of the cytokines involved CD4+ T helper cell expansion and polarization Naiumlve CD4+ T cells can differentiate intoone of three lineages of effector T helper (Th) cells - Th1 Th2 and Th17 - following signaling via the T cell receptor and co-stimulatoryreceptors The effector Th cell populations are defined based upon their cytokine production profile and perform distinct immunoregulatoryfunctions Th1 cells assist in regulating antigen presentation and cell-mediated immunity Anti-parasite and humoral immunity is regulated bythe cytokines produced by Th2 effector cells The cytokines produced by the Th17 subset regulate an inflammatory response


Page 9 of 18

In addition to understanding the paracrine action ofbiochemical cues the cell level also focuses on under-standing how organ-specific system behavior (eg a pri-mary immune response within a secondary lymphoidorgan) emerges from the collective action of cell popula-tions that exhibit slight variation in phenotype In addi-tion to the regulatory cytokines T cell responses arealso regulated by antigen recognition Collectively thefrequency of T cells that recognize specific epitopesinfluences the quality of immune response [132133] Inaddition heterogeneity in T cell commitment may beresponsible for the observed plasticity in the immunepolarization to the recognized epitopes [134] On thetumor side cellular heterogeneity within cells of atumor has been recognized for several decades [135]More recently genomic techniques have providedinsight into the early genetic heterogeneity in dissemi-nated tumor cells compared to cells of the primarytumor [136] However measuring the evolution in cellu-lar heterogeneity in clinical samples has been a particu-lar challenge [137]In cell populations that carry the same genes cellular

heterogeneity can be attributed to two primary sourcesFirst variability in cellular response can be attributed toheterogeneity in expression and activity of proteinsinvolved in the signaling pathways that facilitate cellulardecision-making This heterogeneity is observed in simi-lar cell populations using polychromatic flow cytometry[138] In addition the regulatory proteins that facilitatethis transfer of information may be expressed in lowabundance [139] As the concentration of interactingregulatory proteins decreases the discrete nature of pro-tein-protein interactions becomes more apparent andgives rise to random fluctuations in the informationtransfer process Thus even in cells that exhibit thesame number of regulatory proteins cellular responsesto the same stimulus may be phenotypically different[140] These internal sources of cellular variability aredefined as ldquointrinsicrdquo sourcesSecond variation in the local microenvironment that

surrounds each cell within a population may contributeto variations in collective cellular response The sourcesof cellular heterogeneity that are external to the cell aredefined as ldquoextrinsicrdquo sources Experimental approachessuch as 3-D cell culture provide methods to explore howthese extrinsic sources influence cellular response [141]While the study of intrinsic sources of heterogeneity hasbeen studied by several groups (eg [142143]) extrinsicsources may have greater impact on cellular variabilitythan intrinsic sources due to the simultaneous influenceof external cues on many signaling pathways within a cell[144] Collectively these external cues reflect the compo-sition of stromal and immune cells within the tumormicroenvironment The composition of immune cells the

tumor microenvironment correlate with clinical responseto tumor immunotherapy For instance overall survivalin Head and Neck Squaemous Cell Carcinoma patientstreated with IL-12 correlate with an increased presenceof CD56+ NK cells within the primary tumor irrespectiveof IL-12 treatment [145] In addition impressive infiltra-tion of CD20+ B cells around the tumor was observed insome IL-12 treated patients Understanding how animmune response is coordinated leads to the next levelsthe organ and patient levels

The Organ LevelAnti-tumor immunity is a dynamic process coordinatedvia cellular interactions distributed in time and spaceThe organ level represents the time and length scalesassociated with an adaptive immune response The timeassociated with developing and maintaining immunolo-gical memory is the primary focus of this timescale andspans days to years Control of an immune response isdistributed among different organs of the body wherebyspecific cells perform different functions in each organand the migration of cells between organs enables thetransfer of information As an example of a cell typethat conveys information among organs consider thedendritic cellAs the sentinels of the immune system dendritic cells

(DCs) play an important role in initiating and maintain-ing T cell responses such as T-helper cell polarization[146147] The precise role played by DC in de novo acti-vation of T cells is the culmination of a series of stepsdistributed across both space and time These sequentialsteps as shown graphically in Figure 5 include therecruitment into the peripheral tissue capture of antigenand ldquoeducationrdquo in a peripheral tissue and trafficking to adraining lymph node In the process of migrating fromthe peripheral tissue to a draining lymph node DCsundergo a series of phenotypic changes in cell surfacemarker expression that are collectively called DC matura-tion Proteins expressed on the cell surface enable a cellto sense and respond to its environment These dynamicchanges in DC proteins indicate that the particular cellu-lar response of a DC to the environmental context ishighly dependent on the DCrsquos particular maturationalage Upon arrival to the draining lymph node mature DCinitiate an appropriate T cell response by presenting anti-gen upregulating costimulatory ligands and releasingmediators such as IL-12As recently summarized [148149] the production of

IL12p70 IL12p40 and IL12(p40)2 by mature DC in thedraining lymphoid organ is highly dependent on thecellsrsquo cumulative exposure to inflammatory mediatorsduring differentiation and maturation [150] and thusprovide a link between the peripheral tissues and lym-phoid organs These studies highlight the difficulty in


0 of 18

ascribing biological roles to biochemical cues basedupon in vitro studies alone The simulations suggestthat the combination of both IL-4 and IFN-g in the per-ipheral tissues significantly increases the polarization ofnaiumlve CD4+ T cells towards a Th1 phenotype As wassuggested by Hochrein et al [151] the impact of IL-4on DC education suggests an indirect promotion of Th1polarization In contrast it is stated frequently that IL-4promotes the Th2 polarization of naive CD4+ T cells[130] However the Th2 polarization potential of IL-4 isbased primarily upon the direct action of IL-4 andIFN-g on naiumlve CD4 + T cells observed in vitro Thisresult highlights the pleotropic nature of IL-4 wherebythe spatial restriction in IL-4 expression may differen-tially influence CD4+ T cell polarizationUnder normal conditions cells of the immune system

inhibit tumor growth and progression through the recog-nition and rejection of malignant cells a process calledimmunosurveillance However the immune systemsculpts tumor development by selecting for malignantvariants that create an immunosuppressive microenvir-onment thereby blocking productive antitumor immu-nity This collective process is referred to as cancerimmunoediting [12] This shift in immune behavior fromimmunosurveillance to immunotolerance to a tumor isshown schematically in Figure 5B Tumors promote

tolerance by producing biochemical cues that suppressimmune function including TGF-b IL-6 IL-10 andprostaglandin E2 [152153] Upon metastasis the bio-chemical cues secreted by tumor cells can directly inter-fere with the cellular communication necessary foreliciting an appropriate immune response For instanceTGF-b inhibits the biological activities induced by IL-12[154] through an undefined mechanism [155] In addi-tion IL-6 has been shown to downregulate IL-12Rb2expression in primary polyclonal plasmablastic andmultiple myeloma cells [156]While still localized to the primary site biochemical

cues secreted by the tumor can indirectly bias T cellresponse through their influence on DC education Forinstance many tumors express elevated levels of cycloox-ygenase-2 which is essential for the synthesis of prosta-glandin E2 (PGE2) [157-159] PGE2 exhibits cross talkwith IL-4 and IFN-g during DC differentiation andmaturation such that PGE2 may promote Th2 polariza-tion even in the presence of IL-4 and IFN-g [149] Invitro PGE2 has also been shown to modulate characteris-tics of DC maturation including upregulation of the che-mokine receptor CCR7 [160] essential for homing tosecondary lymphoid organs and inhibition of DC differ-entiation [161] However the in vivo significance of theseeffects of PGE2 on differentiation and maturation has not

Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode

ldquoEducatedrdquoDendritic

CellsldquoUneducatedrdquoDendriticCells

CirculatorySystem

LymphNode

Carcinoma

StromaCell-mediated Cytotoxicity NK

Cell

A B


Cells

ldquoUneducatedrdquoDendriticCells

BIochemical cues in tumor microenvironment influence DC education

Figure 5 A schematic diagram of the multi-organ process involved in immunosurveillance that becomes dysregulated in cancer (A)Immature dendritic cells are recruited into peripheral tissues from the circulation While in the peripheral tissues biochemical cues within thetissue microenvironment educate immature DC ldquoEducatedrdquo mature DC downregulate tissue homing and upregulate chemokine receptors thatpromote DC emigration to the draining lymph node Within the draining lymph node mature DC present antigen express costimulatorymolecules and secrete cytokines that influence T cell activation and polarization The particular profile of cytokines secreted by mature DC isimprinted on immature DC while being educated in the peripheral tissues (B) The presence of an epithelial tumor alters the profile ofbiochemical cues used to educate immature DC within the tissue microenvironment In addition the presence of metastatic tumor cells withinthe draining lymph nodes may interfere with the role that mature DC play in orchestrating an immune response Therapeutic antibodiespromote antibody-dependent cell-mediated cytotoxicity Increased cell death by the carcinoma provides an additional source of tumor-associated antigens for immature DC to present in the draining lymph node


Page 11 of 18

been demonstrated The expansion in the diversity ofantibodies against tumor-associated antigens highlightsthe functional role that an integrated immune system canplay in cancer remission [162-164] Cancer immu-notherapies can be viewed as a mechanism to induce anadaptive response against tumor antigens [165] Thereare multiple points where tumors may interrupt this inte-grated process In vitro study may identify protein-leveland cell-level mechanisms by which tumors manipulateimmunity However inferring how these protein-leveland cell-level mechanisms combine to influence systembehavior from observations obtained at the organ andpatient levels is a particular challenge and is one of themost pervasive problems in the analysis of physiologicalsystems [166]In engineering this problem is called an identification

problem where causal relationships between systemcomponents are inferred from a set of input and outputmeasurements [166] In this context an input may beantibodies against tumor-specific epitopes and an outputmay be tumor regression Many approaches exist for theidentification of simple single-input-single-output(SISO) systems In addition many experimental studiescharacterize how isolated components of physiologicalsystems respond to inputsHowever approaches for identifying causal relation-

ships among components of more complex closed-loopsystems like the immune system are less well devel-oped Typically a closed-loop system is defined as amulti-component system where the output (ieresponse) of one component provides the input (iestimulus) to another component A schematic diagramof a closed-loop system comprised of two componentsis shown in Figure 6 Closed-loop systems are particu-larly challenging as it is impossible to identify the rela-tionships among components of a system based uponoverall input (eg peptide-pulsed DC vaccines) and out-put (eg tumor regression) measurements One of thereasons for this is that changes in the internal state ofthe system may alter the response of the system to adefined input such that there is not a direct relationshipbetween overall system input and output Historicallythe causal mechanisms underlying the behavior ofclosed-loop systems in physiology have been identifiedvia ingenious methods for isolating components withinthe integrated system (ie ldquoopening the looprdquo) A classicexample of this is the discovery of insulin and its role inconnecting food intake to substrate metabolism Asinsulin is only produced by the endocrine pancreas themeasurement of plasma insulin provides a direct mea-surement of the communication between food intakeand substrate metabolism in the peripheral tissues Thepancreas can then be approximated as a SISO systemwhere the glucose concentration in the portal vein is the

input and insulin release into the plasma is the outputas depicted in the Minimal Model for the regulation ofblood glucose [167] Measuring insulin changesin response to changes in glucose provide the basis forpartitioning alterations in system response (ie diabetes)into deficiencies in insulin production (ie type 1 dia-betes) and insulin action (ie type 2 diabetes) Treat-ment for diabetes is tailored to the deficiency incomponent function that exists in the patientBy opening the loop a closed-loop system is reduced

to a series of connected SISO components Opening theloop in the context of tumor immunity may refer to thedynamic measurement of internal states of the DC sub-system in vivo including blood precursor populationsbiochemical cues produced in the tumor microenviron-ment and characteristics of DC that traffic to the drain-ing lymph node In conjunction with knowledge of theT cell repertoire this would enable one to develop amore quantitative view of tumor escape mechanisms(ie how differences in central repertoire selection locallymph node cytokine production and DC educationcollectively influence the quality and magnitude of anti-tumor adaptive immunity) In vivo imaging techniquesare starting to provide some of these details [168] In

Component1

Component2

Closed-loop System

Open-loop System

InputOutput

Figure 6 A schematic diagram of a two-component closed-loop system The behavior of a closed-loop system enclosedwithin the blue dotted box is characterized by measurements ofvariables that provide input to and that reflect the output of theoverall system These variables are depicted as lines that cross thesystem boundary depicted by the dotted blue box The internalvariables that are not observed facilitate communication among thesystem components Output variables for one component mayprovide input variables for another component This internalcommunication may alter system behavior such that the samesystem input may result in different system output depending onthe internal state of the system Measurement of internal variablesenables characterizing the causal relationships between inputvariables and output variables for a specific component within anintact system Ideally measuring these internal variables reducescomplex closed-loop system to a series of connected open-loopsystems as depicted by the red dot-dashed boxes In an open-loopsystem changes in input variables result in a defined response ofthe system


Page 12 of 18

addition peptide- protein- and cell-level knowledge canbe encoded using computational tools in the form ofmultiscale models to aid in interpreting higher levelobservations such as in vivo measurements

Translating Knowledge into the ClinicIn summary cancer is a complex disease manifested bymultiple changes in physiology distributed across a vari-ety of time and length scales In the previous sectionsdetails associated with the role of IL-12 in tumor immu-nology have been described across these time and lengthscales Variations within each of these levels propagateupward to reflect the variability in etiology of cancer andin clinical response to treatment at the patient level Rea-lization of individually tailored therapies requires identi-fying the underlying mechanistic basis for the clinicalphenotype A high degree of uncertainty is associatedwith determining such a mechanistic basis due to thelimitations of experimental observation Prior informa-tion obtained from preclinical studies encoded in mathe-matical models can be used to help interpret the limitedinformation that can be obtained from the patients asencouraged by the Food and Drug Administration [169]In engineering parlance this process is analogous to

systems design a complement to systems analysis Insystems design our knowledge of the putative importantcomponents is used to assess how well mechanisticdescriptions of these components recapitulate realsystem behavior In immunology a major hurdle fordevelop immunotherapies is integrating the knowledgeobtained about individual molecules and cells to predictimmune response [170] In engineering mathematics isused represent our knowledge of the components andsimulation is used to create an expectation for how weexpect the system to behave An underlying theme inthis review is the use of theory and simulation to buildcomputational bridges across scalesRecently multiscale mathematical models have been

used to help understand immunity to infectious patho-gens [171] tumor invasion [172] receptor tyrosinekinase signaling [173] type 1 diabetes [174] and type2 diabetes [175] Integration of biological informationacross scales using multiscale models to predict clinicaloutcomes is an emerging field described as systemsmedicine [176] Despite these examples one mightsuggest that building multiscale models is a futile exer-cise given the uncertainty in the biological detailsassociated with many of the time and length scalesdescribed hereYet models play a central role in science [177] One

frequently creates a mental model of how one thinks asystem behaves (ie a hypothesis) and creates a test(ie an experiment) to see whether the mental modelis a valid representation of the system The causal

relationships implicitly encoded within a mental modelare frequently depicted using a diagram or cartoonGiven the complexity of biological systems mathemati-cal models that incorporate mechanistic informationprovide value as they require an explicit statement ofunderlying assumptions and establish formal relation-ships between cause and effect Creating a mechanisticmodel can also be useful in systems for which ourknowledge is limited Ultimately mechanism-basedmathematical models make predictions what do weexpect to happen in a particular system under particu-lar conditions given our current understanding of howthe components of the system operate If there isagreement between the observed data and the modelpredictions the mechanistic model provides a causalexplanation for the observed behavior Conversely dif-ferences between the expected behaviors and observeddata identify areas where our understanding of the sys-tem is inadequate and reveal novel aspects of biology[118] Thus mathematical models extend our reason-ing abilities by predicting the consequence of assump-tions that may not be interpreted or understoodthrough human intuition alone This is analogous toexperimental equipment such as a flow cytometer thatextend human senses to observe phenomena [178]

ConclusionsIn closing molecular targeted therapies have revolutio-nized the treatment of cancer However developingthese drugs is challenging due to the frequent lack ofclinical efficacy and emergent resistance Shortcomingsin the development of these compounds may be attribu-ted to an inability to translate information among scales(eg how an in vitro assay correlates with clinicalresponse) Understanding the relevance of scales is acentral theme in science that transcends disciplinaryboundaries [177] This review was intended help educatereaders to the diversity of time and length scales thatunderpin cancer pathophysiology Interleukin-12 wasused as an illustrative example to guide the readerthrough these concepts as it bridges innate to adaptiveimmunity and exerts potent antitumor activity Thusdrawing attention to the diversity of time and lengthscales at work in a patient may improve our understand-ing of cancer and lead to the design of immunotherapiesthat are more effective

AcknowledgementsThis work was supported by grants from the PhRMA Foundation theNational Cancer Institute R15CA132124 and the National Institute of Allergyand Infectious Diseases R56AI076221 The content is solely the responsibilityof the author and does not necessarily represent the official views of theNational Cancer Institute the National Institute of Allergy and InfectiousDiseases or the National Institutes of Health The author thanks Dr JonathanL Bramson for his critical reading of this manuscript


Page 13 of 18

Author details1Department of Chemical Engineering and Mary Babb Randolph CancerCenter West Virginia University Morgantown WV 26506-6102 USA2Department of Microbiology Immunology amp Cell Biology West VirginiaUniversity Morgantown WV 26506-6102 USA

Authorsrsquo contributionsDJK conceived drafted finalized and approved the final manuscript

Authorsrsquo informationDJK received his PhD in Chemical Engineering from NorthwesternUniversity and is currently an Assistant Professor in the Department ofChemical Engineering and the Department of Microbiology Immunologyand Cell Biology at West Virginia University Prior to his current position DJKdeveloped multiscale disease models in the areas of atopic asthmarheumatoid arthritis type 1 diabetes and type 2 diabetes for Entelos Inc(Foster City CA httpwwwenteloscom) Entelos is a life sciences companythat through predictive biosimulation helps bring therapeutics to marketfaster

Competing interestsDJK holds stock from Entelos Inc The content is solely the responsibility ofthe author and has not been influenced by Entelos Inc

Received 10 March 2010 Accepted 15 September 2010Published 15 September 2010

References1 Cobleigh MA Vogel CL Tripathy D Robert NJ Scholl S Fehrenbacher L

Wolter JM Paton V Shak S Lieberman G Slamon DJ Multinational studyof the efficacy and safety of humanized anti-HER2 monoclonal antibodyin women who have HER2-overexpressing metastatic breast cancer thathas progressed after chemotherapy for metastatic disease J Clin Oncol1999 172639-2648

2 Slamon DJ Leyland-Jones B Shak S Fuchs H Paton V Bajamonde AFleming T Eiermann W Wolter J Pegram M Baselga J Norton L Use ofchemotherapy plus a monoclonal antibody against HER2 for metastaticbreast cancer that overexpresses HER2 N Engl J Med 2001 344783-792

3 Slamon DJ Godolphin W Jones LA Holt JA Wong SG Keith DE Levin WJStuart SG Udove J Ullrich A et al Studies of the HER-2neu proto-oncogene in human breast and ovarian cancer Science 1989244707-712

4 Cho HS Mason K Ramyar KX Stanley AM Gabelli SB Jr Leahy DJ Structureof the extracellular region of HER2 alone and in complex with theHerceptin Fab Nature 2003 421756-760

5 Franklin MC Carey KD Vajdos FF Leahy DJ Vos AM Sliwkowski MXInsights into ErbB signaling from the structure of the ErbB2-pertuzumabcomplex Cancer Cell 2004 5317-328

6 Yarden Y Biology of HER2 and Its Importance in Breast Cancer Oncology2001 611-13

7 Cardoso F Piccart MJ Durbecq V DiLeo A Resistance to trastuzumab anecessary evil or a temporary challenge Clin Breast Cancer 20023247-257

8 Nahta R Esteva FJ HER2 therapy molecular mechanisms of trastuzumabresistance Breast Cancer Res 2006 8215

9 Jones KL Buzdar AU Evolving novel anti-HER2 strategies Lancet Oncol2009 101179-1187

10 Weiner LM Dhodapkar MV Ferrone S Monoclonal antibodies for cancerimmunotherapy Lancet 2009 3731033-1040

11 Dunn GP Bruce AT Ikeda H Old LJ Schreiber RD Cancer immunoeditingfrom immunosurveillance to tumor escape Nat Immunol 2002 3991-998

12 Dunn GP Old LJ Schreiber RD The three Es of cancer immunoeditingAnnu Rev Immunol 2004 22329-360

13 National Cancer Institute NCI Immunotherapy Agent WorkshopProceedings Annu Rev Immunol 2007 [httpdcbncinihgovImmunAgentWorkindexcfm] Accessed November 25 2009

14 Gately MK Renzetti LM Magram J Stern AS Adorini L Gubler U Presky DHThe interleukin-12interleukin-12-receptor system role in normal andpathologic immune responses Annu Rev Immunol 1998 16495-521

15 Trinchieri G Interleukin-12 and the regulation of innate resistance andadaptive immunity Nat Rev Immunol 2003 3133-146

16 Murphy FJ Hayes MP Burd PR Disparate intracellular processing ofhuman IL-12 preprotein subunits atypical processing of the P35 signalpeptide J Immunol 2000 164839-847

17 Heinzel FP Hujer AM Ahmed FN Rerko RM In vivo production andfunction of IL-12 p40 homodimers J Immunol 1997 1584381-4388

18 Ha SJ Chang J Song MK Suh YS Jin HT Lee CH Nam GH Choi G Choi KYLee SH Kim WB Sung YC Engineering N-glycosylation mutations in IL-12enhances sustained cytotoxic T lymphocyte responses for DNAimmunization Nat Biotechnol 2002 20381-386

19 Ling P Gately MK Gubler U Stern AS Lin P Hollfelder K Su C Pan YCHakimi J Human IL-12 p40 homodimer binds to the IL-12 receptor butdoes not mediate biologic activity J Immunol 1995 154116-127

20 Klinke DJ The Ratio of P40 Monomer to Dimer is an ImportantDeterminant of IL-12 Bioactivity J Theor Biol 2006 240323-335

21 Colombo MP Trinchieri G Interleukin-12 in anti-tumor immunity andimmunotherapy Cytokine Growth Factor Rev 2002 13155-168

22 Bekaii-Saab TS Roda JM Guenterberg KD Ramaswamy B Young DCFerketich AK Lamb TA Grever MR Shapiro CL W E Carson I A phase I trialof paclitaxel and trastuzumab in combination with interleukin-12 inpatients with HER2neu-expressing malignancies Mol Cancer Ther 200982983-2991

23 Parihar R Nadella P Lewis A Jensen R De HC Dierksheide JEVanBuskirk AM Magro CM Young DC Shapiro CL W E Carson I A phase Istudy of interleukin 12 with trastuzumab in patients with humanepidermal growth factor receptor-2-overexpressing malignanciesanalysis of sustained interferon gamma production in a subset ofpatients Clin Cancer Res 2004 105027-5037

24 Parihar R Dierksheide J Hu Y Carson WE IL-12 enhances the natural killercell cytokine response to Ab-coated tumor cells J Clin Invest 2002110983-992

25 Rosenberg SA Yang JC Restifo NP Cancer immunotherapy movingbeyond current vaccines Nature Med 2004 10909-915

26 Ahn AC Tewari M Poon CS Phillips RS The limits of reductionism inmedicine Could systems biology offer an alternative PLoS Medicine2006 3709-713

27 Ramkrishna D Amundson NR Mathematics in chemical engineering A 50year introspection AIChE J 2004 507-23

28 Ottino JM New Tools New Outlooks New Opportunities AIChE J 2005511840-1845

29 Vincenti WG What Engineers Know and How They Know It Baltimore JohnHopkins Press 1990

30 Lander ES Weinberg RA Genomics Journey to the Center of BiologyScience 2000 2871777-1782

31 McGraw-Hill McGraw-Hill Concise Encyclopedia of Engineering New YorkMcGraw-Hill Professional 2005

32 Okino MS Mavrovouniotis ML Simplification of chemical reaction systemsby time-scale analysis Chem Eng Commun 1999 176115-131

33 Haken H Synergetics Introduction and Advanced Topics New York NYSpringer-Verlag 2004

34 Delgado J Liao JC Control of metabolic pathways by time-scaleseparation Biosystems 1995 3655-70

35 Jamshidi N Palsson BO Top-down analysis of temporal hierarchy inbiochemical reaction networks PLoS Comput Biol 2008 4e1000177

36 Weisz PB Diffusion and chemical transformation Science 1973179433-440

37 van Osdol W Fujimori K Weinstein JN An analysis of monoclonalantibody distribution in microscopic tumor nodules consequences of aldquobinding site barrierrdquo Cancer Res 1991 514776-4784

38 Thurber GM Zajic SC Wittrup KD Theoretic criteria for antibodypenetration into solid tumors and micrometastases J Nucl Med 200748995-999

39 Anderson AR Quaranta V Integrative mathematical oncology Nat RevCancer 2008 8227-234

40 Asthagiri AR Lauffenburger DA Bioengineering Models of Cell SignalingAnn Rev Biomed Eng 2000 231-53

41 Pawson T Nash P Assembly of Cell Regulatory Systems Through ProteinInteraction Domains Science 2003 300445-452


Page 14 of 18

42 Hilser VJ Biochemistry An ensemble view of allostery Science 2010327653-654

43 Almlof M Aqvist J Smalas AO Brandsdal BO Probing the effect of pointmutations at protein-protein interfaces with free energy calculationsBiophys J 2006 90433-442

44 Jones RB Gordus A Krall JA MacBeath G A quantitative proteininteraction network for the ErbB receptors using protein microarraysNature 2006 439168-174

45 Kaushansky A Gordus A Chang B Rush J MacBeath G A quantitativestudy of the recruitment potential of all intracellular tyrosine residueson EGFR FGFR1 and IGF1R Mol Biosyst 2008 4643-653

46 Gordus A Krall JA Beyer EM Kaushansky A Wolf-Yadlin A Sevecka MChang BH Rush J MacBeath G Linear combinations of docking affinitiesexplain quantitative differences in RTK signaling Mol Syst Biol 2009 5235

47 van Gunsteren WF Bakowies D Baron R Chandrasekhar I Christen MDaura X Gee P Geerke DP Glattli A Hunenberger PH Kastenholz MAOostenbrink C Schenk M Trzesniak D d van V Yu HB Biomolecularmodeling Goals problems perspectives Angew Chem Int Ed Engl 2006454064-4092

48 Picard C Fieschi C Altare F Al-Jumaah S Al-Hajjar S Feinberg J Dupuis SSoudais C Al-Mohsen IZ Genin E Lammas D Kumararatne DS Leclerc TRafii A Frayha H Murugasu B Wah LB Sinniah R Loubser M Okamoto EAl-Ghonaium A Tufenkeji H Abel L Casanova JL Inherited interleukin-12deficiency IL12B genotype and clinical phenotype of 13 patients fromsix kindreds Am J Hum Genet 2002 70336-348

49 Fieschi C Dupuis S Catherinot E Feinberg J Bustamante J Breiman AAltare F Baretto R Le DF Kayal S Koch H Richter D Brezina M Aksu GWood P Al-Jumaah S Raspall M Duarte AJDS Tuerlinckx D Virelizier JLFischer A Enright A Bernhoft J Cleary AM Vermylen C Rodriguez-Gallego C Davies G Blutters-Sawatzki R Siegrist CA Ehlayel MS Novelli VHaas WH Levy J Freihorst J Al-Hajjar S Nadal D M De V Jeppsson OKutukculer N Frecerova K Caragol I Lammas D Kumararatne DS Abel LCasanova JL Low penetrance broad resistance and favorable outcomeof interleukin 12 receptor beta1 deficiency medical and immunologicalimplications J Exp Med 2003 197527-535

50 Kondo N Matsui E Kaneko H Fukao T Teramoto T Inoue R Watanabe MKasahara K Morimoto N Reduced interferon-gamma production andmutations of the interleukin-12 receptor beta(2) chain gene in atopicsubjects Int Arch Allergy Immunol 2001 124117-120

51 Matsui E Kaneko H Fukao T Teramoto T Inoue R Watanabe M Kasahara KKondo N Mutations of the IL-12 receptor beta2 chain gene in atopicsubjects Biochem Biophys Res Commun 1999 266551-555

52 Baxter EJ Scott LM Campbell PJ East C Fourouclas N Swanton SVassiliou GS Bench AJ Boyd EM Curtin N Scott MA Erber WN Green ARAcquired mutation of the tyrosine kinase JAK2 in humanmyeloproliferative disorders Lancet 2005 3651054-1061

53 Hookham MB Elliott J Suessmuth Y Staerk J Ward AC Vainchenker WPercy MJ McMullin MF Constantinescu SN Johnston JA Themyeloproliferative disorder-associated JAK2 V617F mutant escapesnegative regulation by suppressor of cytokine signaling 3 Blood 20071094924-4929

54 Shaw MH Boyartchuk V Wong S Karaghiosoff M Ragimbeau J Pellegrini SMuller M Dietrich WF Yap GS A natural mutation in the Tyk2pseudokinase domain underlies altered susceptibility of B10QJ mice toinfection and autoimmunity Proc Natl Acad Sci USA 200310011594-11599

55 Sigurdsson S Nordmark G Goring HH Lindroos K Wiman AC Sturfelt GJonsen A Rantapaa-Dahlqvist S Moller B Kere J Koskenmies S Widen EEloranta ML Julkunen H Kristjansdottir H Steinsson K Alm G Ronnblom LSyvanen AC Polymorphisms in the tyrosine kinase 2 and interferonregulatory factor 5 genes are associated with systemic lupuserythematosus Am J Hum Genet 2005 76528-537

56 Hellquist A Jarvinen TM Koskenmies S Zucchelli M Orsmark-Pietras CBerglind L Panelius J Hasan T Julkunen H DrsquoAmato M Saarialho-Kere UKere J Evidence for genetic association and interaction between theTYK2 and IRF5 genes in systemic lupus erythematosus J Rheumatol 2009361631-1638

57 Shimoda K Kato K Aoki K Matsuda T Miyamoto A Shibamori MYamashita M Numata A Takase K Kobayashi S Shibata S Asano YGondo H Sekiguchi K Nakayama K Nakayama T Okamura T Okamura SNiho Y Nakayama K Tyk2 plays a restricted role in IFN alpha signaling

although it is required for IL-12-mediated T cell function Immunity 200013561-571

58 Nakamura R Shibata K Yamada H Shimoda K Nakayama K Yoshikai YTyk2-signaling plays an important role in host defense againstEscherichia coli through IL-23-induced IL-17 production by gammadeltaT cells J Immunol 2008 1812071-2075

59 Sachs K Perez O er D Lauffenburger DA Nolan GP Causal protein-signaling networks derived from multiparameter single-cell data Science2005 308523-529

60 Schlessinger J Epidermal Growth Factor Receptor Pathway Sci Signal(Connections Map in the Database of Cell Signaling as seen 26 July2010)

61 Bhalla US Iyengar R Emergent properties of networks of biologicalsignaling pathways Science 1999 283381-387

62 Bhalla US Models of cell signaling pathways Curr Opin Genet Dev 200414375-381

63 Murray PJ The JAK-STAT signaling pathway input and outputintegration J Immunol 2007 1782623-2629

64 Szabo SJ Dighe AS Gubler U Murphy KM Regulation of the interleukin(IL)-12R beta 2 subunit expression in developing T helper 1 (Th1) andTh2 cells J Exp Med 1997 185817-824

65 Lawless VA Zhang S Ozes ON Bruns HA Oldham I Hoey T Grusby MJKaplan MH Stat4 regulates multiple components of IFN-gamma-inducingsignaling pathways J Immunol 2000 1656803-6808

66 Becskei A Grusby MJ Contribution of IL-12R mediated feedback loop toTh1 cell differentiation FEBS Lett 2007 5815199-5206

67 Fujimoto M Tsutsui H Yumikura-Futatsugi S Ueda H Xingshou O Abe TKawase I Nakanishi K Kishimoto T Naka T A regulatory role forsuppressor of cytokine signaling-1 in T(h) polarization in vivo IntImmunol 2002 141343-1350

68 Eyles JL Metcalf D Grusby MJ Hilton DJ Starr R Negative regulation ofinterleukin-12 signaling by suppressor of cytokine signaling-1 J BiolChem 2002 27743735-43740

69 Yamamoto K Yamaguchi M Miyasaka N Miura O SOCS-3 inhibits IL-12-induced STAT4 activation by binding through its SH2 domain to theSTAT4 docking site in the IL-12 receptor beta2 subunit Biochem BiophysRes Commun 2003 3101188-1193

70 Athie-Morales V Smits HH Cantrell DA Hilkens CM Sustained IL-12signaling is required for Th1 development J Immunol 2004 17261-69

71 OrsquoShea JJ Murray PJ Cytokine signaling modules in inflammatoryresponses Immunity 2008 28477-487

72 Schmidt D Muller S PIASSUMO new partners in transcriptionalregulation Cell Mol Life Sci 2003 602561-2574

73 Wormald S Hilton DJ Inhibitors of cytokine signal transduction J BiolChem 2004 279821-824

74 Arora T Liu B He H Kim J Murphy TL Murphy KM Modlin RL Shuai KPIASx is a transcriptional co-repressor of signal transducer and activatorof transcription 4 J Biol Chem 2003 27821327-21330

75 Lazebnik Y Can a biologist fix a radio Or what I learned while studyingapoptosis Cancer Cell 2002 2179-183

76 Huang CY Jr JEF Ultrasensitivity in the mitogen-activated protein kinasecascade Proc Natl Acad Sci USA 1996 9310078-10083

77 Westerhoff HV Signalling control strength J Theor Biol 2008 252555-56778 Bartel DP MicroRNAs target recognition and regulatory functions Cell

2009 136215-23379 Mayr C Bartel DP Widespread shortening of 3rsquoUTRs by alternative

cleavage and polyadenylation activates oncogenes in cancer cells Cell2009 138673-684

80 Lu TX Munitz A Rothenberg ME MicroRNA-21 is up-regulated in allergicairway inflammation and regulates IL-12p35 expression J Immunol 20091824994-5002

81 Navarro A Diaz T Martinez A Gaya A Pons A Gel B Codony C Ferrer GMartinez C Montserrat E Monzo M Regulation of JAK2 by miR-135aprognostic impact in classic Hodgkin lymphoma Blood 20091142945-2951

82 Jiang S Zhang HW Lu MH He XH Li Y Gu H Liu MF Wang EDMicroRNA-155 functions as an OncomiR in breast cancer by targetingthe suppressor of cytokine signaling 1 gene Cancer Res 2010703119-3127

83 Cozen W Gill PS Salam MT Nieters A Masood R Cockburn MGGauderman WJ Martinez-Maza O Nathwani BN Pike MC Berg DJVD


Page 15 of 18

Hamilton AS Deapen DM Mack TM Interleukin-2 interleukin-12 andinterferon-gamma levels and risk of young adult Hodgkin lymphomaBlood 2008 1113377-3382

84 Zhao B Meng LQ Huang HN Pan Y Xu QQ A novel functionalpolymorphism 16974 AC in the interleukin-12-3rsquo untranslated region isassociated with risk of glioma DNA Cell Biol 2009 28335-341

85 Wei YS Lan Y Luo B Lu D Nong HB Association of variants in theinterleukin-27 and interleukin-12 gene with nasopharyngeal carcinomaMol Carcinog 2009 48751-757

86 Han SS Cho EY Lee TS Kim JW Park NH Song YS Kim JG Lee HPKang SB Interleukin-12 p40 gene (IL12B) polymorphisms and the risk ofcervical cancer in Korean women Eur J Obstet Gynecol Reprod Biol 200814071-75

87 Takeuchi-Hatanaka K Ohyama H Nishimura F Kato-Kogoe N Soga YMatsushita S Nakasho K Yamanegi K Yamada N Terada N Takashiba SPolymorphisms in the 5rsquo flanking region of IL12RB2 are associated withsusceptibility to periodontal diseases in the Japanese population J ClinPeriodontol 2008 35317-323

88 Remmers EF Plenge RM Lee AT Graham RR Hom G Behrens TW deBakker PI Le JM Lee HS Batliwalla F Li W Masters SL Booty MG Carulli JPPadyukov L Alfredsson L Klareskog L Chen WV Amos CI Criswell LASeldin MF Kastner DL Gregersen PK STAT4 and the risk of rheumatoidarthritis and systemic lupus erythematosus N Engl J Med 2007357977-986

89 Hirschfield GM Liu X Xu C Lu Y Xie G Lu Y Gu X Walker EJ Jing KJuran BD Mason AL Myers RP Peltekian KM Ghent CN Coltescu CAtkinson EJ Heathcote EJ Lazaridis KN Amos CI Siminovitch KA Primarybiliary cirrhosis associated with HLA IL12A and IL12RB2 variants N EnglJ Med 2009 3602544-2555

90 Sato K Shiota M Fukuda S Iwamoto E Machida H Inamine T Kondo SYanagihara K Isomoto H Mizuta Y Kohno S Tsukamoto K Strong Evidenceof a Combination Polymorphism of the Tyrosine Kinase 2 Gene and theSignal Transducer and Activator of Transcription 3 Gene as a DNA-BasedBiomarker for Susceptibility to Crohnrsquos Disease in the JapanesePopulation J Clin Immunol 2009 29815-825

91 Rowley JD Chromosome translocations dangerous liaisons revisited NatRev Cancer 2001 1245-250

92 Korbel JO Urban AE Grubert F Du J Royce TE Starr P Zhong GNEmanuel BS Weissman SM Snyder M Gerstein MB Systematic predictionand validation of breakpoints associated with copy-number variants inthe human genome Proc Natl Acad Sci USA 2007 10410110-10115

93 Korbel JO Urban AE Affourtit JP Godwin B Grubert F Simons JF Kim PMPalejev D Carriero NJ Du L Taillon BE Chen ZT Tanzer A Saunders ACEChi JX Yang FT Carter NP Hurles ME Weissman SM Harkins TTGerstein MB Egholm M Snyder M Paired-end mapping reveals extensivestructural variation in the human genome Science 2007 318420-426

94 Zhao X Li C Paez JG Chin K Janne PA Chen TH Girard L Minna JChristiani D Leo C Gray JW Sellers WR Meyerson M An integrated viewof copy number and allelic alterations in the cancer genome usingsingle nucleotide polymorphism arrays Cancer Res 2004 643060-3071

95 Esteller M Epigenetics in cancer N Engl J Med 2008 3581148-115996 Airoldi I Cocco C Di CE Disaro S Ognio E Basso G Pistoia V Methylation

of the IL-12Rbeta2 gene as novel tumor escape mechanism for pediatricB-acute lymphoblastic leukemia cells Cancer Res 2006 663978-3980

97 Suzuki M Iizasa T Nakajima T Kubo R Iyoda A Hiroshima K Nakatani YFujisawa T Aberrant methylation of IL-12Rbeta2 gene in lungadenocarcinoma cells is associated with unfavorable prognosis Ann SurgOncol 2007 142636-2642

98 Schoeberl B Eichler-Jonsson C Gilles ED Muumlller G Computationalmodeling of the dynamics of the MAP kinase cascade activated bysurface and internalized EGF receptors Nature Biotech 2002 20370-376

99 Kholodenko BN Demin OV Moehren G Hoek JB Quantification of ShortTerm Signaling by the Epidermal Growth Factor Receptor J Biol Chem1999 27430169-30181

100 Birtwistle MR Hatakeyama M Yumoto N Ogunnaike BA Hoek JBKholodenko BN Ligand-dependent responses of the ErbB signalingnetwork experimental and modeling analyses Mol Syst Biol 2007 3144

101 Forsythe R Mavrovouniotis M Model Reduction in the ComputationalModeling of Reaction Systems J Chem Inf Comput Sci 1997 37258-264

102 Broadbelt LJ Pfaendtner J Lexicography of kinetic modeling of complexreaction networks AIChE J 2005 512112-2121

103 Green WH Predictive Kinetics A New Approach for the 21st CenturyAdv Chem Eng 2007 321-50

104 Ugi I Bauer J Brandt J Freidrich J Gasteiger J Jochum C Schubert W Newapplications of computers in chemistry Angew Chem Int Ed Engl 197918111-123

105 Klinke DJ Broadbelt LJ Mechanism Reduction during ComputerGeneration of Compact Reaction Models AIChE J 1997 431828-1837

106 Klinke DJ Broadbelt LJ Construction of a Mechanistic Model of Fischer-Tropsch Synthesis on Ni(111) and Co(0001) Surfaces Chem Eng Sci 1999543379-3389

107 Blinov ML Faeder JR Goldstein B Hlavacek WS BioNetGen software forrule-based modeling of ignal transduction based on the interactions ofmolecular domains Bioinform 2004 203289-3291

108 Fages F Soliman S Chabrier-Rivier N Modelling and querying interactionnetworks in the biochemical abstract machine BIOCHAM J Biol PhysChem 2004 464-73

109 Lok L Brent R Automatic generation of cellular reaction networks withMoleculizer 10 Nat Biotechnol 2005 23131-136

110 Meier-Schellersheim M Xu X Angermann B Kunkel EJ Jin T Germain RNKey role of local regulation in chemosensing revealed by a newmolecular interaction-based modeling method PLoS Comput Biol 2006 2e82

111 Blinov ML Faeder JR Goldstein B Hlavacek WS A Network Model of EarlyEvents in Epidermal Growth Factor Receptor Signaling That Accounts forCombinatorial Complexity Biosystems 2006 83136-151

112 Hlavacek WS Faeder JR Blinov ML Perelson AS Goldstein B TheComplexity of Complexes in Signal Transduction Biotech Bioeng 200384783-794

113 Susnow RG Dean AM Green WH Broadbelt LJ Rate-Based Constructionof Kinetic Models for Complex Systems J Phys Chem A 19971013731-3740

114 Klinke DJ Signal transduction networks in cancer quantitativeparameters influence network topology Cancer Res 2010 701773-1782

115 Klinke DJ An empirical Bayesian approach for model-based inference ofcellular signaling networks BMC Bioinformatics 2009 10371

116 Banga JR Optimization in computational systems biology BMC SystemsBiology 2008 247

117 Gelman A Carlin JB Stern HS Rubin DB Bayesian Data Analysis Texts inStatistical Science Boca Raton FL Chapman and Hall 2004

118 National Research Council (US) Committee on Learning How people learnbrain mind experience and school Washington DC National AcademiesPress 2000

119 Brown KS Sethna JP Statistical mechanical approaches to models withmany poorly known parameters Phys Rev E Stat Nonlin Soft Matter Phys2003 68021904

120 Finley SD Gupta D Cheng N Klinke DJ Inferring Relevant ControlMechanisms for Interleukin-12 Signaling within Naive CD4+ T cellsImmunol Cell Biol

121 Jacobson NG Szabo SJ Weber-Nordt RM Zhong Z Schreiber RD J EDarnell J Murphy KM Interleukin 12 signaling in T helper type 1 (Th1)cells involves tyrosine phosphorylation of signal transducer andactivator of transcription (Stat)3 and Stat4 J Exp Med 19951811755-1762

122 Nimmerjahn F Ravetch JV Divergent immunoglobulin g subclass activitythrough selective Fc receptor binding Science 2005 3101510-1512

123 Hart DN Dendritic cells unique leukocyte populations which control theprimary immune response Blood 1997 903245-3287

124 Moser M Murphy KM Dendritic cell regulation of TH1-TH2 developmentNat Immunol 2000 1199-205

125 Aggarwal S Ghilardi N Xie MH de Sauvage FJ Gurney AL Interleukin-23promotes a distinct CD4 T cell activation state characterized by theproduction of interleukin-17 J Biol Chem 2003 2781910-1914

126 Langrish CL Chen Y Blumenschein WM Mattson J Basham B Sedgwick JDMcClanahan T Kastelein RA Cua DJ IL-23 drives a pathogenic T cellpopulation that induces autoimmune inflammation J Exp Med 2005201233-240

127 Oppmann B Lesley R Blom B Timans JC Xu Y Hunte B Vega F Yu NWang J Singh K Zonin F Vaisberg E Churakova T Liu M Gorman DWagner J Zurawski S Liu Y Abrams JS Moore KW Rennick D de Waal-Malefyt R Hannum C Bazan JF Kastelein RA Novel p19 protein engages


Page 16 of 18

IL-12p40 to form a cytokine IL-23 with biological activities similar aswell as distinct from IL-12 Immunity 2000 13715-725

128 Jang MS Son YM Kim GR Lee YJ Lee WK Cha SH Han SH Yun CHSynergistic production of interleukin-23 by dendritic cells derived fromcord blood in response to costimulation with LPS and IL-12 J Leukoc Biol2009 86691-699

129 Martin-Orozco N Dong C The IL-17IL-23 axis of inflammation in cancerfriend or foe Curr Opin Investig Drugs 2009 10543-549

130 Seder RA Paul WE Acquisition of lymphokine-producing phenotype byCD4+ T cells Annu Rev Immunol 1994 12635-673

131 Worschech A Kmieciak M Knutson KL Bear HD Szalay AA Wang EMarincola FM Manjili MH Signatures associated with rejection orrecurrence in HER-2neu-positive mammary tumors Cancer Res 2008682436-2446

132 Rizzuto GA Merghoub T Hirschhorn-Cymerman D Liu C Lesokhin AMSahawneh D Zhong H Panageas KS Perales MA tan Bonnet GWolchok JD Houghton AN Self-antigen-specific CD8+ T cell precursorfrequency determines the quality of the antitumor immune response JExp Med 2009 206849-866

133 Moon JJ Chu HH Pepper M McSorley SJ Jameson SC Kedl RMJenkins MK Naive CD4(+) T cell frequency varies for different epitopesand predicts repertoire diversity and response magnitude Immunity2007 27203-213

134 Murphy KM Stockinger B Effector T cell plasticity flexibility in the face ofchanging circumstances Nat Immunol 2010 11674-680

135 Fidler IJ Kripke ML Metastasis Results from Preexisting Variant CellsWithin a Malignant Tumor Science 1977 197893-895

136 Gangnus R Langer S Breit E Pantel K Speicher MR Genomic Profiling ofViable and Proliferative Micrometastatic Cells from Early-Stage BreastCancer Patients Clin Cancer Res 2004 103457-3464

137 Weinberg RA The Biology of Cancer New York NY Garland Science 2007138 Irish JM Hovland R Krutzik PO Perez OD Bruserud O Gjertsen BT

Nolan GP Single cell profiling of potentiated phospho-protein networksin cancer cells Cell 2004 118217-228

139 Swamy M Kulathu Y Ernst S Reth M Schamel WWA Two dimensionalBlue Native-SDS-PAGE analysis of SLP family adaptor proteincomplexes Immunol Letters 2006 104131-137

140 Losick R Desplan C Stochasticity and cell fate Science 2008 32065-68141 Debnath J Brugge JS Modelling glandular epithelial cancers in three-

dimensional cultures Nat Rev Cancer 2005 5675-688142 McAdams HH Arkin A Stochastic mechanisms in gene expression Proc

Natl Acad Sci USA 1997 94814-819143 Feinerman O Veiga J Dorfman JR Germain RN tan Bonnet G Variability

and robustness in T cell activation from regulated heterogeneity inprotein levels Science 2008 3211081-1084

144 Elowitz MB Levine AJ Siggia ED Swain PS Stochastic gene expression ina single cell Science 2002 2971183-1186

145 Herpen CMV van der Laak JA V de I van Krieken JH de Wilde PCBalvers MG Adema GJ Mulder PHD Intratumoral recombinant humaninterleukin-12 administration in head and neck squamous cellcarcinoma patients modifies locoregional lymph node architecture andinduces natural killer cell infiltration in the primary tumor Clin CancerRes 2005 111899-1909

146 Banchereau J Briere F Caux C Davoust J Lebecque S Liu YJ Pulendran BPalucka K Immunobiology of dendritic cells Annu Rev Immunol 200018767-811

147 Lanzavecchia A Sallusto F The instructive role of dendritic cells on T cellresponses lineages plasticity and kinetics Curr Opin Immunol 200113291-298

148 Klinke DJ An Age-Structured Model of Dendritic Cell Trafficking in theLung Am J Physiol Lung Cell Mol Physiol 2006 2911038-1049

149 Klinke DJ A Multi-scale Model of Dendritic Cell Education and Traffickingin the Lung Implications for T Cell Polarization Ann Biomed Eng 200735937-955

150 Ebner S Ratzinger G Krosbacher B Schmuth M Weiss A Reider DKroczek RA Herold M Heufler C Fritsch P Romani N Production of IL-12by human monocyte-derived dendritic cells is optimal when thestimulus Is given at the onset of maturation and Is further enhanced byIL-4 [In Process Citation] J Immunol 2001 166633-641

151 Hochrein H OrsquoKeeffe M Luft T Vandenabeele S Grumont RJ Maraskovsky EShortman K Interleukin (IL)-4 is a major regulatory cytokine governing

bioactive IL-12 production by mouse and human dendritic cells J ExpMed 2000 192823-833

152 Nicolini A Carpi A Rossi G Cytokines in breast cancer Cytokine GrowthFactor Rev 2006 17325-337

153 Ben-Baruch A Host microenvironment in breast cancer developmentinflammatory cells cytokines and chemokines in breast cancerprogression reciprocal tumor-microenvironment interactions BreastCancer Res 2003 531-36

154 Bright JJ Sriram S TGF-beta inhibits IL-12-induced activation of Jak-STATpathway in T lymphocytes J Immunol 1998 1611772-1777

155 Sudarshan C Galon J Zhou Y OrsquoShea JJ TGF-beta does not inhibit IL-12-and IL-2-induced activation of Janus kinases and STATs J Immunol 19991622974-2981

156 Airoldi I Cocco C Giuliani N Ferrarini M Colla S Ognio E Taverniti G Di CECutrona G Perfetti V Rizzoli V Ribatti D Pistoia V Constitutive expressionof IL-12R beta 2 on human multiple myeloma cells delineates a noveltherapeutic target Blood 2008 112750-759

157 Soslow RA Dannenberg AJ Rush D Woerner BM Khan KN Masferrer JKoki AT COX-2 is expressed in human pulmonary colonic andmammary tumors Cancer 2000 892637-2645

158 Chan G Boyle JO Yang EK Zhang F Sacks PG Shah JP Edelstein DSoslow RA Koki AT Woerner BM Masferrer JL Dannenberg AJCyclooxygenase-2 expression is up-regulated in squamous cellcarcinoma of the head and neck Cancer Res 1999 59991-994

159 Ristimaki A Honkanen N Jankala H Sipponen P Harkonen M Expressionof cyclooxygenase-2 in human gastric carcinoma Cancer Res 1997571276-1280

160 Luft T Jefford M Luetjens P Toy T Hochrein H Masterman KAMaliszewski C Shortman K Cebon J Maraskovsky E Functionally distinctdendritic cell (DC) populations induced by physiologic stimuliprostaglandin E(2) regulates the migratory capacity of specific DCsubsets Blood 2002 1001362-1372

161 Sinha P Clements VK Fulton AM Ostrand-Rosenberg S Prostaglandin E2promotes tumor progression by inducing myeloid-derived suppressorcells Cancer Res 2007 674507-4513

162 Vanderlugt CL Miller SD Epitope spreading in immune-mediateddiseases implications for immunotherapy Nat Rev Immunol 2002 285-95

163 Disis ML Wallace DR Gooley TA Dang Y Slota M Lu H Coveler ALChilds JS Higgins DM Fintak PA dela RC Tietje K Link J Waisman JSalazar LG Concurrent trastuzumab and HER2neu-specific vaccination inpatients with metastatic breast cancer J Clin Oncol 2009 274685-4692

164 Wierecky J Muller MR Wirths S Halder-Oehler E Dorfel D Schmidt SMHantschel M Brugger W Schroder S Horger MS Kanz L Brossart PImmunologic and clinical responses after vaccinations with peptide-pulsed dendritic cells in metastatic renal cancer patients Cancer Res2006 665910-5918

165 Adams GP Weiner LM Monoclonal antibody therapy of cancer NatBiotechnol 2005 231147-1157

166 Khoo MCK Physiological Control Systems Analysis Simulation and EstimationIEEE Press Series on Biomedical Engineering Piscataway NJ IEEE Press 2000

167 Bergman RN Ider YZ Bowden CR Cobelli C Quantitative estimation ofinsulin sensitivity Am J Physiol 1979 236667

168 Catron DM Itano AA Pape KA Mueller DL Jenkins MK Visualizing the first50 hr of the primary immune response to a soluble antigen Immunity2004 21341-347

169 United States Food and Drug Administration Innovation or stagnationchallenge and opportunity on the critical path to new medical products2004 [httpwwwfdagovocinitiativescriticalpathwhitepaperpdf]

170 Abbas AK C A Janeway J Immunology improving on nature in thetwenty-first century Cell 2000 100129-138

171 Kirschner DE Chang ST Riggs TW Perry N Linderman JJ Toward amultiscale model of antigen presentation in immunity Immunol Rev2007 21693-118

172 Quaranta V Rejniak KA Gerlee P Anderson AR Invasion emerges fromcancer cell adaptation to competitive microenvironments quantitativepredictions from multiscale mathematical models Semin Cancer Biol2008 18338-348

173 Costa MN Radhakrishnan K Wilson BS Vlachos DG Edwards JS Coupledstochastic spatial and non-spatial simulations of ErbB1 signalingpathways demonstrate the importance of spatial organization in signaltransduction PLoS One 2009 4e6316


Page 17 of 18

174 Shoda L Kreuwel H Gadkar K Zheng Y Whiting C Atkinson M Bluestone JMathis D Young D Ramanujan S The Type 1 Diabetes PhysioLabPlatform a validated physiologically based mathematical model ofpathogenesis in the non-obese diabetic mouse Clin Exp Immunol 2010161250-267

175 Klinke DJ Integrating Epidemiological Data into a Mechanistic Model ofType 2 Diabetes Validating the Prevalence of Virtual Patients AnnBiomed Eng 2008 36321-324

176 Auffray C Chen Z Hood L Systems medicine the future of medicalgenomics and healthcare Genome Med 2009 12

177 American Association for the Advancement of Science Science for AllAmericans New York Oxford University Press 1990

178 Humphreys P Extending Ourselves Computational Science Empiricism andScientific Method New York NY Oxford University Press 2007

doi1011861476-4598-9-242Cite this article as Klinke A multiscale systems perspective on cancerimmunotherapy and Interleukin-12 Molecular Cancer 2010 9242

Submit your next manuscript to BioMed Centraland take full advantage of

bull Convenient online submission

bull Thorough peer review

bull No space constraints or color figure charges

bull Immediate publication on acceptance

bull Inclusion in PubMed CAS Scopus and Google Scholar

bull Research which is freely available for redistribution

Submit your manuscript at wwwbiomedcentralcomsubmit


Page 18 of 18

Abstract

Introduction

Systems Analysis and Identifying Scales

The Peptide Level

The Protein Level

The Cell Level

The Organ Level

Translating Knowledge into the Clinic

Conclusions

Acknowledgements

Author details

Authors contributions

Authors information

Competing interests

References

hold promise for augmenting antitumor immunotherapy[13]Interleukin-12 (IL-12) is an important immune regu-

latory cytokine that exerts potent antitumor activityand a member of a small family of heterodimeric cyto-kines [1415] In the literature IL12 implicitly refers toa 75-kDa heterodimer that is formed by the disulfide-linkage of two independently regulated gene productsa 40 kDa (p40) subunit and a 35 kDa (p35) subunit[16] The p40 subunit as a homodimer (IL12(p40)2) ormonomer (IL12p40) can also bind to the IL-12 recep-tor resulting in interactions that antagonize IL12p70binding both in mice [1718] and humans [19] Thebioactivity of IL-12 is due to the competitive bindingof all isoforms with the IL-12 receptor [20] In the per-ipheral tissues IL-12 originally called Natural KillerCell Stimulating Factor enhances the ability of NKcells to lyse target cells a mechanism exploited fortumor immunotherapy [21] As an adjuvant IL-12 pro-motes NK-cell mediated killing of HER2-positivetumor cells in patients treated with trastuzumab[22-24] Yet despite the sincere efforts of many tounderstand the complicated relationship between can-cer and the immune system translating the therapeuticpotential of immunotherapies observed in vitro and inanimal models to the clinic has been difficult [25]One of potential sources for this difficulty has been

how we have predominantly approached this problemldquoDivide and conquerrdquo has been used to describe the pre-dominant mode of scientific inquiry in the medicalsciences [26] The underlying assumption is that under-standing the behavior of a complicated system can beachieved by deconstructing the system into more funda-mental components and characterizing the behavior ofthe components In studying the fundamental compo-nents in isolation we may miss collective interactionsthat are important for understanding how the integratedsystem works In addition this reductionist approachtowards scientific inquiry also spawned subdisciplinesthat focus on specific aspects of biological systems Forinstance the study of protein structure and folding typi-cally falls under the purview of biophysics the study ofmetabolic and signaling pathways falls under the purviewof biochemistry and the study of emergent behavior ofpopulations of immune cells to biochemical cues fallsunder the purview of immunology The engineering dis-ciplines have taken a different approach towards under-standing natural and synthetic systems For instancechemical engineering has a rich history where theory andmathematics provide a framework for analyzing design-ing and controlling reacting systems [2728] One of theunifying concepts in the discipline is that theory andmathematics can be extended using simulation Usingsimulation engineers predict the behavior of complicated

systems using knowledge of system components and the-ories (eg transport phenomena and chemical kinetics)that describe how we expect the components to interactThese predictions are then tested experimentally to askthe question is our incomplete knowledge of the systemcomponents sufficient to reconstruct the behavior of thesystem In the process a more fundamental question isasked is this system complicated (ie components inter-act via defined rules that we can characterize in isolation)or is it complex (ie the behavior of components is anemergent behavior that can only be characterized bystudying the integrated system) Collectively this processis a knowledge generating activity [29] This process alsohelps manage uncertainty do we understand the systemsufficiently to make a decision or do we need to gathermore data From this perspective research activities asso-ciated with the disciplines of engineering and basic medi-cal sciences represent contrasting modes for acquiringknowledge about systems (ie reconstruction versusdeconstruction) The objective of this review is todescribe methods used in engineering to study systemsand to analyze cancer immunotherapy from an engineer-ing perspective using IL-12 as an illustrative example

Systems Analysis and Identifying ScalesWhen presented with a complex problem such as devel-oping a novel immunotherapy a common problem-solving approach is to first identify the importantcomponents whose interactions define system behaviorAdvances in molecular biology during the twentiethcentury provided experimental tools to identify the indi-vidual components of complex biological systems [30]Once identified the function of these components andtheir interactions can be characterized In engineeringthis process is called systems analysis [31]Knowledge obtained by systems analysis is coupled to

the experimental techniques that scientists use to probesystems and the computational tools that are used tointerpret those experimental observations One of theparticular techniques used in systems analysis is to iden-tify the different time scales that underpin the responseof a dynamic system (ie a time scale analysis) to anabrupt change in environmental conditions A timescale analysis aids in simplifying the response of asystem by parsing system components and their corre-sponding dynamics into different kinetic manifolds (eg[32]) The evolution in the system is constrained by theslow variables (ie the slow kinetic manifold) while thefast variables (ie the fast kinetic manifold) exist at apseudo-equilibrium Moreover variables that exhibittime scales significantly longer than the time scale overwhich the system has been observed can be consideredstationary (ie a stationary manifold) This phenomenonrelated to separating time scales has been termed the


of 18



=[ ][ ]

D Abk Ag

sdotsdot

o

e o(1)






Page 3 of 18



100

102

104

106

108

1010

10-8

10-6

10-4

10-2

100

102

Time scale (sec)

Leng

th S

cale

(m)

Peptide

Protein

Cell

Patient

Peptid




ClinicalStudies

SNPsGenotype

Data

InferenceD I

D I

D I

D I


Heterogeneity


PopulationResponse


CollapseDynamic




Folding States

IL-2

Dendritic Cells

Naiumlve CD4+

T Cells IL-4

IL-12IFN-

Th2

Th1

IL-2IFN-

IL-4IL-5IL-10IL-13

IL-23IL-17

Th17

IL-2

TDendritic Cells

Naiumlve CD4+

T Cells IL-4

IL-12IFN-

Th2Th2

Th1Th1

IL-2IFN-

IL-4IL-5IL-10IL-13

IL-23IL-17

Th17

Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode

Epithelium

Stroma Fibroblasts

CirculatorySystem


System

LymphNode

Carcinoma

StromaNK Cell

CirculatorySystem

LymphNode

Carcinoma

StromaNK Cell

Oncogenesis

Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode


CCC



a





Epithelium

Stroma Fibroblasts

CirculatorySystem


System

LymphNode

Carcinoma

StromaNK Cell



ee




LymphNode

Carcinoma

StromaNK Cell

Oncogenesis

Organ

lt

Leng

th S

cale

(m)



Page 4 of 18







Page 5 of 18




AS RS

kd Dka

RS =

2 1

1

sdotsdot +

(2)

p40 p35

BOX1 BOX1

BOX2

811

804

757

TYK2 JAK2

IL12Rβ2IL12Rβ1

PP

STAT4P

SOCS

SOCS PTP

PIAS

N-PTP



STAT4

STAT4P P

STAT4

STAT4P P

STAT4

STAT4

STAT4

STAT4

Cofactors

+


Cytosol

Nucleus

IL12Rβ2



Page 6 of 18








Signaling Protein 1

(S1)

RS1Complex

Receptor(R)


(I)


(A)


Production)



ka

kd



Page 7 of 18









Page 8 of 18





IL-2



IL-12IFN-γ

Th2

Th1

IFN-γ

IL-4IL-5IL-13


Effe

ctor

CD

4+ T

cel

ls

TGFβ IL-6



Page 9 of 18









Page 10 of 18





Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode



CirculatorySystem

LymphNode

Carcinoma


Cell

A B


Cells





Page 11 of 18






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



Page 12 of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References



=[ ][ ]

D Abk Ag

sdotsdot

o

e o(1)






of 18



100

102

104

106

108

1010

10-8

10-6

10-4

10-2

100

102

Time scale (sec)

Leng

th S

cale

(m)

Peptide

Protein

Cell

Patient

Peptid




ClinicalStudies

SNPsGenotype

Data

InferenceD I

D I

D I

D I


Heterogeneity


PopulationResponse


CollapseDynamic




Folding States

IL-2

Dendritic Cells

Naiumlve CD4+

T Cells IL-4

IL-12IFN-

Th2

Th1

IL-2IFN-

IL-4IL-5IL-10IL-13

IL-23IL-17

Th17

IL-2

TDendritic Cells

Naiumlve CD4+

T Cells IL-4

IL-12IFN-

Th2Th2

Th1Th1

IL-2IFN-

IL-4IL-5IL-10IL-13

IL-23IL-17

Th17

Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode

Epithelium

Stroma Fibroblasts

CirculatorySystem


System

LymphNode

Carcinoma

StromaNK Cell

CirculatorySystem

LymphNode

Carcinoma

StromaNK Cell

Oncogenesis

Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode


CCC



a





Epithelium

Stroma Fibroblasts

CirculatorySystem


System

LymphNode

Carcinoma

StromaNK Cell



ee




LymphNode

Carcinoma

StromaNK Cell

Oncogenesis

Organ

lt

Leng

th S

cale

(m)



Page 4 of 18







Page 5 of 18




AS RS

kd Dka

RS =

2 1

1

sdotsdot +

(2)

p40 p35

BOX1 BOX1

BOX2

811

804

757

TYK2 JAK2

IL12Rβ2IL12Rβ1

PP

STAT4P

SOCS

SOCS PTP

PIAS

N-PTP



STAT4

STAT4P P

STAT4

STAT4P P

STAT4

STAT4

STAT4

STAT4

Cofactors

+


Cytosol

Nucleus

IL12Rβ2



Page 6 of 18








Signaling Protein 1

(S1)

RS1Complex

Receptor(R)


(I)


(A)


Production)



ka

kd



Page 7 of 18









Page 8 of 18





IL-2



IL-12IFN-γ

Th2

Th1

IFN-γ

IL-4IL-5IL-13


Effe

ctor

CD

4+ T

cel

ls

TGFβ IL-6



Page 9 of 18









Page 10 of 18





Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode



CirculatorySystem

LymphNode

Carcinoma


Cell

A B


Cells





Page 11 of 18






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



Page 12 of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References



100

102

104

106

108

1010

10-8

10-6

10-4

10-2

100

102

Time scale (sec)

Leng

th S

cale

(m)

Peptide

Protein

Cell

Patient

Peptid




ClinicalStudies

SNPsGenotype

Data

InferenceD I

D I

D I

D I


Heterogeneity


PopulationResponse


CollapseDynamic




Folding States

IL-2

Dendritic Cells

Naiumlve CD4+

T Cells IL-4

IL-12IFN-

Th2

Th1

IL-2IFN-

IL-4IL-5IL-10IL-13

IL-23IL-17

Th17

IL-2

TDendritic Cells

Naiumlve CD4+

T Cells IL-4

IL-12IFN-

Th2Th2

Th1Th1

IL-2IFN-

IL-4IL-5IL-10IL-13

IL-23IL-17

Th17

Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode

Epithelium

Stroma Fibroblasts

CirculatorySystem


System

LymphNode

Carcinoma

StromaNK Cell

CirculatorySystem

LymphNode

Carcinoma

StromaNK Cell

Oncogenesis

Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode


CCC



a





Epithelium

Stroma Fibroblasts

CirculatorySystem


System

LymphNode

Carcinoma

StromaNK Cell



ee




LymphNode

Carcinoma

StromaNK Cell

Oncogenesis

Organ

lt

Leng

th S

cale

(m)



of 18







Page 5 of 18




AS RS

kd Dka

RS =

2 1

1

sdotsdot +

(2)

p40 p35

BOX1 BOX1

BOX2

811

804

757

TYK2 JAK2

IL12Rβ2IL12Rβ1

PP

STAT4P

SOCS

SOCS PTP

PIAS

N-PTP



STAT4

STAT4P P

STAT4

STAT4P P

STAT4

STAT4

STAT4

STAT4

Cofactors

+


Cytosol

Nucleus

IL12Rβ2



Page 6 of 18








Signaling Protein 1

(S1)

RS1Complex

Receptor(R)


(I)


(A)


Production)



ka

kd



Page 7 of 18









Page 8 of 18





IL-2



IL-12IFN-γ

Th2

Th1

IFN-γ

IL-4IL-5IL-13


Effe

ctor

CD

4+ T

cel

ls

TGFβ IL-6



Page 9 of 18









Page 10 of 18





Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode



CirculatorySystem

LymphNode

Carcinoma


Cell

A B


Cells





Page 11 of 18






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



Page 12 of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References







of 18




AS RS

kd Dka

RS =

2 1

1

sdotsdot +

(2)

p40 p35

BOX1 BOX1

BOX2

811

804

757

TYK2 JAK2

IL12Rβ2IL12Rβ1

PP

STAT4P

SOCS

SOCS PTP

PIAS

N-PTP



STAT4

STAT4P P

STAT4

STAT4P P

STAT4

STAT4

STAT4

STAT4

Cofactors

+


Cytosol

Nucleus

IL12Rβ2



Page 6 of 18








Signaling Protein 1

(S1)

RS1Complex

Receptor(R)


(I)


(A)


Production)



ka

kd



Page 7 of 18









Page 8 of 18





IL-2



IL-12IFN-γ

Th2

Th1

IFN-γ

IL-4IL-5IL-13


Effe

ctor

CD

4+ T

cel

ls

TGFβ IL-6



Page 9 of 18









Page 10 of 18





Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode



CirculatorySystem

LymphNode

Carcinoma


Cell

A B


Cells





Page 11 of 18






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



Page 12 of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References




AS RS

kd Dka

RS =

2 1

1

sdotsdot +

(2)

p40 p35

BOX1 BOX1

BOX2

811

804

757

TYK2 JAK2

IL12Rβ2IL12Rβ1

PP

STAT4P

SOCS

SOCS PTP

PIAS

N-PTP



STAT4

STAT4P P

STAT4

STAT4P P

STAT4

STAT4

STAT4

STAT4

Cofactors

+


Cytosol

Nucleus

IL12Rβ2



of 18








Signaling Protein 1

(S1)

RS1Complex

Receptor(R)


(I)


(A)


Production)



ka

kd



Page 7 of 18









Page 8 of 18





IL-2



IL-12IFN-γ

Th2

Th1

IFN-γ

IL-4IL-5IL-13


Effe

ctor

CD

4+ T

cel

ls

TGFβ IL-6



Page 9 of 18









Page 10 of 18





Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode



CirculatorySystem

LymphNode

Carcinoma


Cell

A B


Cells





Page 11 of 18






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



Page 12 of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References








Signaling Protein 1

(S1)

RS1Complex

Receptor(R)


(I)


(A)


Production)



ka

kd



of 18









Page 8 of 18





IL-2



IL-12IFN-γ

Th2

Th1

IFN-γ

IL-4IL-5IL-13


Effe

ctor

CD

4+ T

cel

ls

TGFβ IL-6



Page 9 of 18









Page 10 of 18





Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode



CirculatorySystem

LymphNode

Carcinoma


Cell

A B


Cells





Page 11 of 18






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



Page 12 of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References









of 18





IL-2



IL-12IFN-γ

Th2

Th1

IFN-γ

IL-4IL-5IL-13


Effe

ctor

CD

4+ T

cel

ls

TGFβ IL-6



Page 9 of 18









Page 10 of 18





Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode



CirculatorySystem

LymphNode

Carcinoma


Cell

A B


Cells





Page 11 of 18






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



Page 12 of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References





IL-2



IL-12IFN-γ

Th2

Th1

IFN-γ

IL-4IL-5IL-13


Effe

ctor

CD

4+ T

cel

ls

TGFβ IL-6



of 18









Page 10 of 18





Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode



CirculatorySystem

LymphNode

Carcinoma


Cell

A B


Cells





Page 11 of 18






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



Page 12 of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References









of 18





Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode



CirculatorySystem

LymphNode

Carcinoma


Cell

A B


Cells





Page 11 of 18






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



Page 12 of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References





Epithelium

Stroma Fibroblasts

CirculatorySystem

LymphNode



CirculatorySystem

LymphNode

Carcinoma


Cell

A B


Cells





of 18






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



Page 12 of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References






Component1

Component2

Closed-loop System

Open-loop System

InputOutput



of 18










Page 13 of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References










of 18

















































Page 14 of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References

















































of 18













































Page 15 of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References













































of 18















































Page 16 of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References















































of 18


















































Page 17 of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References


















































of 18
















Page 18 of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References
















of 18

Abstract

Introduction


The Peptide Level

The Protein Level

The Cell Level

The Organ Level


Conclusions

Acknowledgements

Author details


Authors information

Competing interests

References

review open access a multiscale systems perspective on ... · a multiscale systems perspective on...

Documents