Patent Application: US-201113227333-A

Abstract:
the disclosure relates to methods of predicting the effects of therapy , designing / conducting a clinical trial , selecting a subject for a clinical trial , selecting a subject for therapy , monitoring a subject &# 39 ; s responsiveness to therapy , treating a subject , and predicting effects of anti - cd25 therapy .

Description:
aspects of the disclosure relate to predicting the effect of a therapy on a subject prior to treatment . in some embodiments , the effect of a therapy is a binary outcome , i . e . the subject will respond or will not respond to a given therapy . in some embodiments , the effect of a therapy comprises a likelihood of response to a particular therapy , expressed as a percentage or in another format . alternately , the effect of a therapy may comprise a number expressed in arbitrary units such as a “ score .” for instance , a subject has a 50 % chance of responding to therapy . as another example , a subject has a score of 40 . as another example , said score may be reported in connection with a likelihood of response — for instance , subject has a score of 40 , and in clinical trials subjects with a score of 40 had a 70 % chance of responding to therapy . the term respond or responsiveness , may refer to partial or complete responses . responsiveness depends on the condition being treated . in some embodiments , responsiveness comprises the extent to which the therapy is achieving its intended effect , such as , for example , ameliorating the subject from the disease . responsiveness may be based , for example , on reduction in tumor size , progression free survival , complete and durable response , or any basis known to one of ordinary skill in the art . the term therapy is intended to include prophylaxis , amelioration , prevention or cure from the condition being treated . the subject may have not received any therapy before or may have undergone a prior therapy . treatment comprises administering one or more therapies . in some embodiments , the therapy is a single therapeutic / agent , or a therapeutic regimen consisting of multiple therapies / agents . in one embodiment , the therapy comprises a particular therapeutic molecule or molecules to be administered . in some embodiments , therapy comprises a particular molecule , as well as dosing , timing , and other parameters related to the therapy or its administration . in some embodiments , the therapy comprises a therapy already approved by a regulatory agency . in some embodiments , the therapy comprises a therapy under investigation in clinical trials . in some embodiments , the therapy comprises an agonist or an antagonist of a cytokine receptor or a cytokine receptor subunit . in some embodiments , an agonist for a cytokine receptor is a therapy that binds to a cytokine receptor and causes it to generate a signal . in some embodiments , an antagonist for a cytokine receptor is a therapy that blocks the effective functioning of the cytokine receptor , preventing it from generating a signal . in some embodiments , the therapy alters the quantity of ligand available to bind to a cytokine receptor or a cytokine receptor subunit . the subunit may be a protein that comprises all or part of a receptor . often , a subunit is one protein that assembles with one or two other proteins to form a complex that together comprises a receptor . for instance , cd122 is a subunit that assembles with cd132 to form a complex that is the intermediate - affinity il - 2 receptor . in some embodiments , the therapy modulates a pathway triggered by a cytokine receptor or a cytokine receptor subunit . in some embodiments , the cytokine receptor or cytokine receptor subunit comprises one or more of the following : cd25 ( il - 2ralpha ), cd122 ( il - 2rbeta ), cd132 ( gamma chain ), cd 124 ( il - 4ralpha ), cd 127 ( il - 7ralpha ), cd 129 ( il - 9ralpha ), il - 15ralpha , il - 21ralpha ( nilr ), tslpr , il - 13ralpha1 ( cd213alpha1 ), or il - 13ralpha2 ( cd213alpha2 ). in embodiments where the therapy antagonizes a receptor subunit , the expected effect of the therapy comprises a reduction in the quantity of that subunit available to form complexes with other subunits , or to bind to ligand . in embodiments where the therapy alters the quantity of one or more ligands , the expected effect of the therapy comprises an increase or decrease in the quantity of available ligand . in some embodiments , input values are numbers that represent something about a subject before he or she is treated . in other words , numbers that correspond to some characteristic of the subject prior to the administration of therapy . for instance , input values could refer to the quantity of a particular receptor subunit on a particular cell type in a subject . in one example , the input values are used by a computer to determine output values . in some embodiments , providing input values are obtained from or provided by a third party . the third party may provide the values in an electronic format such , for example , as a spreadsheet . in some embodiments , output values are numbers that are determined using the input values , but that represent a different characteristic of the subject than the input values represent . in other words , numbers that represent something about a subject that is different from what the input values represent , but which depends in some way on the input values . for instance , output values could refer to the number of receptor - ligand surface complexes between il - 7 and the il - 7 receptor , when the input values were the concentration of il - 7 in a subject &# 39 ; s serum , and the number of cd127 receptor subunits on a patient &# 39 ; s cd56bright nk cells . in some embodiments , output values are obtained from or provided by a third party . the third party may provide the values in an electronic format such , for example , as a spreadsheet . in some embodiments , signaling on one or more receptor ( s ) comprises the extent to which a receptor activates a chain or cascade of molecular interactions within a cell in response to the binding of a particular ligand to that receptor . in one embodiment , this is represented by the number of receptor - ligand complexes at a given time . in another embodiment , this is represented as the number of receptor - ligand complexes internalized during a given time interval . for a therapy that antagonizes a receptor subunit , in some embodiments , a therapy &# 39 ; s expected expect is a reduction in the quantity of that subunit . for a therapy that alters the quantity of one or more ligands , in some embodiments , a therapy &# 39 ; s expected expect is an increase or decrease in the quantity of available ligand . in some embodiments , the therapy alters the quantity of ligand available . in some embodiments , the therapy increases the amount of ligand that is able to bind to receptors on a subject &# 39 ; s cell ( s ). in some embodiments , the therapy decreases the amount of ligand that is able to bind to receptors on a subject &# 39 ; s cell ( s ). in some embodiments , decreasing the amount of ligand comprises reducing the amount of ligand by depleting it , or causing an agent to bind to it so that it is no longer able to bind to receptors , or applying a therapy that otherwise lessens the availability of the ligand . in some embodiments , increasing the amount comprises adding additional ligand directly ( as in the case of a recombinant cytokine ) or applying a therapy that otherwise increases the availability of the ligand . in some embodiments , the therapy modulates a pathway triggered by a cytokine receptor or by a cytokine receptor subunit . in some embodiments , the alteration changes the magnitude of signaling that is occurring in a cascade of events that involves a particular molecule . in one example , a jak3 inhibitor would be considered to modulate the jak3 pathway because it reduces the magnitude of signaling in the cascade of events that involves jak3 . in some embodiments , a signaling pathway comprises a chain or cascade of molecular interactions occurring within a cell in response to the binding of a particular ligand to a particular receptor . if a therapy is designed to interfere with this chain or interactions , then the subunits of the receptor that initiate that chain of interactions comprise the targeted receptor subunits . for instance , if the therapy is a jak inhibitor , then it targets the jak signaling pathway which is triggered by the cd 132 receptor subunit , and so the targeted receptor subunits would comprise cd132 and any receptor subunits that form complexes with it . in some embodiments , analysis of receptor - ligand binding and trafficking dynamics comprises calculating the extent of signaling that is occurring or will occur on a given receptor as represented by the number of receptor - ligand surface complexes , using measurable input values such as , for example , the number of receptors , the concentration of ligand , and the binding affinity of the ligand for the receptor . such calculations take into account the forward and reverse rates at which a ligand binds to a receptor , as well as the rates at which ligands , receptors , and their complexes move between the cell surface and endosomes . in other words , generating a set of output values from a set of input values whereby the output values are a number of receptor ligand surface complexes , and the process of generating the output values takes into account the association and dissociation rates of ligand and receptor , and the movement of receptors and complexes between the cell surface and endosomes . in some embodiments , analysis assembly dynamics comprises calculating the extent to which receptor subunits come together to form complexes , taking into account the association and dissociation rates with which the various receptor subunits come together to form complexes . in other words , generating a set of output values from a set of input values whereby the output values are a number of receptors composed of two or more particular subunits , and the process of generating the output values takes into account the association and dissociation rates of the various receptor subunits . aspects of the disclosure comprise providing input values for a therapy &# 39 ; s target receptor subunit ( s ). for a therapy that agonizes or antagonizes a receptor subunit , a therapy &# 39 ; s target receptor subunit comprises the receptor subunit ( s ) that it agonizes or antagonizes and any receptor subunit ( s ) that form ( s ) complexes with that receptor unit . in one embodiment , for an anti - cd25 therapy , the target receptor subunits comprises cd25 , cd122 , and cd132 . for a therapy that alters the quantity of one or more ligands , a therapy &# 39 ; s target receptor subunit comprises the receptor subunit ( s ) that bind to said ligand ( s ). for a therapy that modulates a pathway triggered by a receptor or receptor subunit , a therapy &# 39 ; s target receptor subunit comprises the receptor subunit ( s ) that trigger said pathway . aspects of the disclosure comprise providing input values comprising the absolute or relative quantity of receptor units that interact with the therapy &# 39 ; s target receptor unit . in some embodiments , the interaction comprises binding , allosterically modifying , forming complexes with , or causing conformation change ( s ). the methods described herein have important implications for treating subjects and also for the clinical development of new treatments . determining whether a subject will benefit from continued treatment or would benefit from a change in treatment is clinically useful . one example of clinical usefulness of the methods of this invention includes identifying subjects who are less likely or more likely to respond to a treatment . the methods are also useful in predicting or determining that a subject would benefit from continued treatment or would benefit from a change in treatment . health care practitioners and providers select treatment regimens based upon the expected net benefit to the subject . the net benefit is derived from the risk to benefit ratio . the present disclosure permits the determination of whether a subject will benefit from continued treatment or would benefit from a change in treatment , thereby aiding a physician in selecting a treatment . another example of clinical usefulness , in the case of human subjects for example , includes aiding clinical investigators in the selection for clinical trials of subjects with a high likelihood of obtaining a net benefit . it is expected that clinical investigators now will use the present disclosure for determining entry criteria for clinical trials . predicting the effects of an anti - cd25 therapy on a subject prior to treatment in one embodiment , the therapy is an antibody against cd25 . the therapy &# 39 ; s target receptor subunits are cd25 , cd122 , and cd132 . the ligand that interacts with the therapy &# 39 ; s target receptor subunits is il - 2 . the receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are cd124 , cd127 , cd129 , il - 15ralpha , and il - 21ralpha . the ligands that interact with receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are : il - 4 , il - 7 , il - 9 , il - 15 , and il - 21 . the receptor subunits and ligands considered further include tslpr , il - 13ralpha1 , tslp , and il - 13 . the receptor subunits considered further include il - 13ralpha2 . in one embodiment , assaying a sample further comprises utilizing the following protocol adapted from [ cesana , 2006 ], [ venken , 2008 ], [ hatjiharissi , 2007 ] blood collection : whole blood is collected in heparin - containing vacutainer tubes ( bd or equivalent ). determining absolute cell counts : trucount tubes ( bd biosciences or equivalent ) are utilized to determine accurate cell counts . cells are stained with fluorescently labeled antibodies against the following eight makers ( human ): cd3 , cd4 , cd25 , cd127 , cd45ra , cd56 , cd16 , and cd19 . define the five key subsets as follows : cell counts for each subset are determined using a facs aria or facs calibur ( bd biosciences or equivalent ). isolating peripheral blood mononuclear cells ( pbmcs ): pbmcs are isolated from whole blood using ficoll density gradient centrifugation ( histopaque , sigma - aldrich ; amersham ; or equivalent ). cell sorting : relevant subsets are separated . cells are stained with fluorescently labeled antibodies against the following eight makers ( human ): cd3 , cd4 , cd25 , cd127 , cd45ra , cd56 , cd 16 , and cd 19 . the five key subsets are defined as follows : each subset is isolated using a facs aria , facs calibur ( bd biosciences ) or equivalent . cell surface receptor quantification : each of the four facs - sorted cell subsets collected above is stained with phycoerythrin ( pe ) conjugated antibodies against one or more of the following targets : cd25 , cd122 , cd132 , cd124 , cd127 , cd129 , il - 15ralpha , il - 21ralpha , tslpr , il - 13ralpha1 , and il - 13ralpha2 . one or more of the following reagents ( or equivalent ) is utilized : monoclonal anti - human cd25 phycoerythrin ( catalog number fab1020p : r & amp ; d systems , minneapolis , minn . usa ) or pe mouse anti - human cd25 ( catalog number 555432 becton dickinson biosciences , san jose , calif . usa ) monoclonal anti - human il - 2rβ ( cd122 )- phycoerythrin ( catalog number : fab224p r & amp ; d systems , minneapolis , minn . usa ) or pe mouse anti - human cd122 ( catalog number : 554522 becton dickinson biosciences , san jose , calif . usa ) anti - human cd 132 / common γ chain - phycoerythrin monoclonal antibody ( catalog number : ic2841p r & amp ; d systems , minneapolis , minn . usa ) or pe rat anti - human cd132 ( catalog number 555898 becton dickinson biosciences , san jose , calif . usa ) or pe mouse anti - human cd132 ( catalog number 555900 becton dickinson biosciences , san jose , calif . usa ) monoclonal anti - human il - 4 rα ( cd124 )- phycoerythrin ( catalog number : fab230p r & amp ; d systems , minneapolis , minn . usa ) or pe mouse anti - human cd124 ( catalog number 552178 becton dickinson biosciences , san jose , calif . usa ). monoclonal anti - human il - 7 rα / cd127 - phycoerythrin ( catalog number : fab306p r & amp ; d systems , minneapolis , minn . usa ) or pe mouse anti - human cd127 ( catalog number 557938 becton dickinson biosciences , san jose , calif . usa ). monoclonal anti - human il - 9 r - phycoerythrin ( catalog number : fab290p r & amp ; d systems , minneapolis , minn . usa ) or pe anti - human il - 9 receptor ( cd129 ) ( catalog number 310403 biolegend , san diego , calif . usa ). monoclonal anti - human il - 15 rα - phycoerythrin ( catalog number : fab1471p r & amp ; d systems , minneapolis , minn . usa ) or pe anti - human cd359 ( il - 15ra ) antibody ( catalog number 330207 biolegend , san diego , calif . usa ). monoclonal anti - human il - 21 r - phycoerythrin ( catalog number : fab9911p r & amp ; d systems , minneapolis , minn . usa ) or pe mouse anti - human il - 21r ( catalog number 560264 becton dickinson biosciences , san jose , calif . usa ) or pe anti - human cd360 ( il - 21r ) antibody ( catalog number 347805 , biolegend , san diego , calif . usa ). pe anti - human tslpr ( tslp - r ) antibody ( catalog number 322805 , biolegend , san diego , calif . usa ) or phycoerythrin ( pe ) anti - human tslp receptor ( tslpr , thymic stromal derived lymphopoietin receptor ) ( catalog number 12 - 5499 , ebioscience , san diego , calif . usa ). monoclonal anti - human il - 13 rα1 - phycoerythrin ( catalog number : fab1462p r & amp ; d systems , minneapolis , minn . usa ). il13 receptor alpha 2 antibody [ b - d13 ] ( phycoerythrin ) ( catalog number : ab27415 or ab34931 , abcam , cambridge , mass . usa ) the number of receptors per cell for each receptor type are quantified in each cell subset , calibrating using quantibrite pe phycoerythrin fluorescence quantitation beads ( catalog number 340495 : becton dickinson immunocytometry systems , san jose , calif . usa ) using techniques described in [ pannu , 2001 ] and [ hatjiharissi , 2007 ]. alternately , a technique that determines molecules of equivalent soluble fluorescein ( mesf ) is used to determine receptor quantities . intracellular and cell surface receptor quantification : after quantifying only the cell surface receptors using the above procedure , the cells are permeabilized using cytofix / cytoperm ( catalog number 554722 , becton dickinson biosciences , san jose , calif . usa ) or equivalent . then the above “ cell surface receptor quantification ” procedure is repeated , but in this case will yield the total ( intracellular + cell surface ) receptor levels . the intracellular levels is then calculated for each receptor by subtracting the surface levels from the total levels as in [ hodge , 2000 ]. measure cytokine levels : serum cytokine levels are determined as in [ sabatino , 2008 ] using a searchlight multiplex array ( aushon biosystems , billerica , mass . usa ) to measure the concentrations of il - 2 , il - 4 , il - 7 , il - 9 , il - 15 , il - 21 , il - 13 , and tslp in the patient &# 39 ; s serum . while il - 21 is not currently available , it can be measured separately using an elisa kit such as the human il - 21 elisa max ™ deluxe ( catalog number 433804 , biolegend , san diego , calif . usa ) or the human il - 21 elisa ready - set - go ! set ( catalog number 88 - 7216 , ebioscience , san diego , calif . usa ). in one embodiment , the measurements resulting from the above protocols comprise the initial conditions that are input into the computational model as defined in the table below . in this example , cell type a is defined to be cd56bright nk cells , but in other embodiments it could be other cell types , or repeated for multiple cell types . in one embodiment , the method comprises assessing these measured values using a computational model . here we discuss the background for said model . careful work by smith , beginning with a key study in 1984 [ cantrell , 1984 ] and continuing to today , has led to the quantal theory of immunology . this theory predicts that t cells or other lymphocytes will proliferate once the number of formed receptor - ligand complexes , integrated over time , crosses a certain threshold . in the quantal theory , the parameters having the most impact on proliferation time are the number of receptors per cell , the binding affinity of those receptors , and the number of cells present . in addition , the binding and trafficking dynamics have a significant impact . this includes internalization rates , degradation rates , recycling rates , and so forth . lauffenburger and colleagues developed computational models of these binding and trafficking dynamics , and demonstrated the ability to predict cd8 + t cell proliferation in vitro in response to il - 2 [ fallon , 2000 ]. while lauffenburger references smith &# 39 ; s work , he uses a proliferation rate that is based on the instantaneous number of receptor - ligand surface complexes , rather than the integral of these complexes over time . this was a reasonable approximation for the situation that lauffenburger was modeling , in which proliferation had little effect on the outcome , but for modeling cell proliferation following high dose il - 2 - induced lymphopenia it is critical to capture smith &# 39 ; s findings more directly . we therefore substitute a zero proliferation rate , solve for the instantaneous number of receptor - ligand complexes for each receptor type , sum this value over time , and determine which receptor type first reaches the threshold number of complexes , and when . lauffenburger &# 39 ; s model focuses on a single receptor type ( il - 2 ). we made the non - obvious decision to build a model of multiple receptor types competing for the same cd 132 subunit . it is highly non - obvious that such an approach would result in an effective means to predict response to therapy . fig1 illustrates the receptor subunit and cytokine interactions upon which the model equations are based . fig1 ( a ) shows the portion of the interactions involving the il - 9 receptor . fig1 ( b ) shows the portion of the interactions involving the il - 21 receptor . fig1 ( c ) shows the portion of the interactions involving the il - 4 and il - 13 receptors . fig1 ( d ) shows the portion of the interactions involving the il - 7 and tslp receptors . fig1 ( e ) shows the portion of the interactions involving the il - 2 receptor . fig1 ( f ) shows the portion of the interactions involving the il - 15 receptor . in one particular embodiment , the following format is used to define relevant parameters to represent interactions : kf_x_y is defined as the surface forward rate constant of x binding to y . kr_x_y is defined as the surface reverse rate constant of x binding to y . kfe_x_y is defined as the internal forward rate constant of x binding to y . kre_x_y is defined as the internal reverse rate constant of x binding to y . ksyn_x_y is defined as the rate at which x in synthesized in response to the binding event indicated in y . kt_celltypea_x is defined as the constitutive internalization rate of x on cell type a . ke_celltypea_x is defined as the internalization rate of x on cell type a . kh_celltypea_x is defined as the degradation rate of x on cell type a . kx_celltypea_x is defined as the recycling rate of x on cell type a . vs_celltypea_x is defined as the rate at which x is synthesized on cell type a . veff is defined as an effective volume in order to modify the three dimensional equations to properly represent the two dimensional interactions between receptor subunits in a membrane . in one particular embodiment , using the above format to define parameters , the following parameters are provided from literature values as indicated , although in other embodiments other values may be used or the values may be measured : veff =( 4 * pi *( 5e - 6 )̂ 2 )*( 1e - 9 )* 1000 ;% effective volume ( liters per cell ) for 2d 1000 l / m ̂ 3 . 5 um radius . 10 nm height . kf_cd25_cd122 =( 1 /( na * veff )* kr_cd25_cd122 / 278 ;% nm ̂- 1 min ̂- 1 [ rickert , 2004 ] kfe_cd25_cd122 = 0 ;% does not occur —[ fallon , 2000 ]— all cd25 dissociates kre_cd25_cd122 = 1000000 ;% set arbitrarily high because —[ fallon , 2000 ]— all cd25 dissociates kf_il2_cd122_cd132 = kr_il2_cd122_cd132 / 1 . 1 ;% exact number scaled from [ fallon , 2000 ]. range confirmed by [ voss , 1992 ] kre_il2_cd122_cd132 = 8 * kr_il2_cd122_cd132 ;% [ fallon , 2000 ] kfe_il2_cd122_cd132 = kre_il2_cd122_cd132 / 1 ;%[ fallon , 2000 ] expressed in nm instead of pm kf_il2_cd25_cd122_cd132 = kr_il2_cd25_cd122_cd132 / 0 . 011 ;% exact number from [ fallon , 2000 ]. range confirmed by [ voss , 1992 ] kfe_il2_cd25_cd122_cd132 = 0 ;% does not occur —[ fallon , 2000 ]— all cd25 dissociates kre_il2_cd25_cd122_cd132 = 1000000 ;% set arbitrarily high because —[ fallon , 2000 ]— all cd25 dissociates kr_cd25_cd122_cd132 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_cd25_cd122_cd132 = 0 ;% kre_cd25_cd122_cd132 = 1000000 ;% set arbitrarily high because —[ fallon , 2000 ]— all cd25 dissociates kf_il2_cd122 = kr_il2_cd122 / 144 ;% nma - 1 min ̂- 1 [ rickert , 2004 ] but [ myszka , 1996 ] says 450 nm — 2 citations kre_il2_cd122 = 8 * kr_il2_cd122 ;% use same proportions as il - 2 binding to cd122 / cd132 complex from [ fallon , 2000 ] kfe_il2_cd122 = kre_il2_cd122 / 1 ;% use same proportions as il - 2 binding to cd122 / cd132 complex from [ fallon , 2000 ] kf_cd122_il2_cd25 =( 1 /( na * veff )* kr_cd122_il2_cd25 / 63 ;% nma - 1 min ̂- 1 [ rickert , 2004 ] kfe_cd122_il2_cd25 = 0 ;% does not occur —[ fallon , 2000 ]— all cd25 dissociates kre_cd122_il2_cd25 = 1000000 ;% set arbitrarily high because —[ fallon , 2000 ]— all cd25 dissociates , so no complexes kf_il2_cd25 = kr_il2_cd25 / 10 ;% nma - 1 min ̂- 1 [ rickert , 2004 ] [ myszka , 1996 ] agrees kfe_il2_cd25 = 0 ;% does not occur —[ fallon , 2000 ]— all cd25 dissociates kre_il2_cd25 = 1000000 ;% set arbitrarily high because —[ fallon , 2000 ]— all cd25 dissociates , so no complexes kf_cd25_il2_cd122_cd132 =( 1 /( na * veff )* kf_il2_cd25 ;% assume same binding affinity as cd25 to free il - 2 . stickiest interaction , and assume cd122 / cd132 doesn &# 39 ; t significantly add or interfere . kr_cd25_il2_cd122_cd132 = kr_il2_cd25 ;% min ̂- 1 , assume same binding affinity as cd25 to free il - 2 kfe_cd25_il2_cd122_cd132 = 0 ;% does not occur —[ fallon , 2000 ]— all cd25 dissociates kre_cd25_il2_cd122_cd132 = 1000000 ;% set arbitrarily high because —[ fallon , 2000 ]— all cd25 dissociates , so no complexes kf_il2_cd25_cd122 = kr_il2_cd25_cd122 / 0 . 4 ;% nm ̂- 1 min ̂- 1 , [ myska , 1996 ]— 0 . 2 - 0 . 6 nm kfe_il2_cd25_cd122 = 0 ;% does not occur —[ fallon , 2000 ]— all cd25 dissociates kre_il2_cd25_cd122 = 1000000 ;% set arbitrarily high because —[ fallon , 2000 ]— all cd25 dissociates , so no complexes kf_cd25_il2_cd122 =( 1 /( na * veff )* kf_il2_cd25 ;% assume same binding affinity as il - 2 to free cd25 . stickiest interaction , and assume cd122 doesn &# 39 ; t significantly add or interfere . kr_cd25_il2_cd122 = kr_il2_cd25 ;% min ̂- 1 , assume same binding affinity as il - 2 to free cd25 . stickiest interaction , and assume cd122 doesn &# 39 ; t significantly add or interfere . kfe_cd25_il2_cd122 = 0 ;% does not occur —[ fallon , 2000 ]— all cd25 dissociates kre_cd25_il2_cd122 = 1000000 ;% set arbitrarily high because —[ fallon , 2000 ]— all cd25 dissociates , so no complexes kf_il15_cd122_cd132 = kf_il2_cd122_cd132 ;% crucial interaction — presented in trans from other cells . 1 . 1 nm similar affinity to il - 2 for cd122 / cd132 [ vamosi , 2004 ] kf_il15_il5r = kr_il15_il5r / 0 . 05 ;% nma - 1 min ̂- 1 ( kd = 5 × 10 ̂- 11 ) [ mortier , 2008 ] kre_il15_il5r = 8 * kr_il15_il15r ;% min ̂- 1 , use same proportions as il - 2 binding to cd122 / cd132 complex from [ fallon , 2000 ] kfe_il15_il15r = kre_il15_il15r / 1 ;% use same proportions as il - 2 binding to cd122 / cd132 complex from [ fallon , 2000 ] kf_cd122_cd132_il15_il15r =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_cd122_cd132_il15_il15r = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_cd122_cd132_il15_il15r = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd122_cd132_il15_il15r = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kf_il15r_cd122_cd132 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_il15r_cd122_cd132 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_il15r_cd122_cd132 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_il15r_cd122_cd132 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kf_il15r_cd122 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_il15r_cd122 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_il15r_cd122 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_il15r_cd122 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kf_il15il15r_cd122 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_il15_il15r_cd122 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_il15_il15r_cd122 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_il15_il15r_cd122 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kf_cd122_il15_il15r =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_cd122_il15_il15r = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_cd122_il15_il15r = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd122_il15il15r = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kf_il15r_il15_cd122 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_il15r_il15_cd122 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_il15r_il15_cd122 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_il15r_il15_cd122 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kf_il15r_il15_cd122_cd132 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_il15r_il15_cd122_cd132 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_il15r_il15_cd122_cd132 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_il15r_il15_cd122_cd132 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kf_il15_cd132 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kfe_il15_cd132 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_il7_cd127_cd132 = kr_il7_cd127_cd132 / 0 . 08 ;% nma - 1 min ̂- 1 80 pm [ olosz , 2000 ]— kfe_il7_cd127_cd132 = 0 ;% kre_il7_cd127_cd132 = 0 ;% kf_il7_cd127 = kr_il7_cd127 / 56 ;% nm ̂- 1 min ̂- 1 glycosylated , otherwise = kr_il7_cd127 / 18000 ( 18 um ) unglycosylated —[ olosz , 2000 ]: 200 pm kfe_il7_cd127 = 0 ;% kre_il7_cd127 = 0 ;% kf_il4ra_cd132 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_il4ra_cd132 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_il4ra_cd132 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_il4ra_cd132 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_cd124_cd132 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_cd124_cd132 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_cd124_cd132 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd124_cd132 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_cd124_cd213 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_cd124_cd213 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_cd124_cd213 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd124_cd213 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_il4_cd124_cd132 = kr_il4_cd124_cd132 / 1100 ;% nma - 1 min ̂- 1 ( kd = 1 . 1 um : [ andrews , 2006 ]) kfe_il4_cd124_cd132 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_il4_cd124_cd132 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_il13_cd213 = kr_il13_cd213 / 37 . 8 ;% nma - 1 min ̂- 1 , [ andrews , 2002 ] [ kraich , 2006 agrees ] kfe_il13_cd213 = 0 ;% kre_il13_cd213 = 0 ;% kf_il13_cd124_cd213 = kf_il13_cd213 ;% “ the ka value obtained . . . was similar to that obtained for the binding of 1 ′- 13 to il - 13ra1 [ andrews , 2002 ] kf_il4_cd124 = kr_il4_cd124 /( 0 . 150 );% nma - 1 min ̂- 1 , ( zhang , 2003 says 150 pm , kraich , 2006 agrees ) ([ andrews , 2006 ] says 382 pm ) kfe_il4_cd124 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_il4_cd124 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_il4_cd124_cd213 = kf_il4_cd124 ;% “ presence of il - 13ra1 had no detectable effect on the binding of il - 4 to il - 4ra ” [ andrews , 2002 ] kr_il4_cd124_cd213 = kr_il4_cd124 ;% min ̂- 1 , “ presence of il - 13ra1 had no detectable effect on the binding of il - 4 to il - 4ra ” [ andrews , 2002 ] kfe_il4_cd124_cd213 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_il4_cd124_cd213 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_il13_cd124 = 1 ;% min ̂- 1 , placeholder , no direct binding observed [ andrews , 2002 ] kfe_il13_cd124 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_il13_cd124 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_cd124_il4_cd213 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_cd124_il4_cd213 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_cd124_il4_cd213 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd124_il4_cd213 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_cd124_il13_cd213 =( 1 /( na * veff )* kr_cd124_il13_cd213 / 150 ;% [ kraich , 2006 ] kfe_cd124_il13_cd213 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd124_il13_cd213 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_il4_cd213 = 0 ;% no direct binding observed [ andrews , 2006 ] or kd = 2500 nm [ kraich , 2006 ] kr_il4_cd213 = 1 ;% min ̂- 1 , placeholder , no direct binding observed [ andrews , 2006 ] kfe_il4_cd213 = 0 ;% kre_il4_cd213 = 0 ;% kf_cd213_il13_cd124 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_cd213_il13_cd124 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_cd213_il13_cd124 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd213_il13_cd124 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_cd213_il4_cd124 =( 1 /( na * veff )* kr_cd213_il4_cd124 /( 1200 );% [ kraich , 2006 ] kfe_cd213_il4_cd124 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd213_il4_cd124 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_il9_cd129_cd132 = kr_il9_cd129_cd132 / 0 . 1 ;% nm ̂- 1 min ̂- 1 kd = 100 pm [ de smedt , 2000 ] kfe_il9_cd129_cd132 = 0 ;% kre_il9_cd129_cd132 = 0 ;% kf_il21_il21r = kr_il21_il21r /( 0 . 070 );% nm ̂- 1 min ̂- 1 70 pm [ zhang 2003 ] kfe_il21_il21r = 0 ;% kre_il21_il21r = 0 ;% kr_cd132_il4_il4ra = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_cd132_il4_il4ra = 0 ;% temp leave as zero [ bielekova , 2006 ] kre_cd132_il4_il4ra = 0 ;% temp leave as zero b / c [ bielekova , 2006 ] kf_cd132_il7_cd127 =( 1 /( na * veff )* kr_cd132_il7_cd127 / 12 ;% nm ̂- 1 min ̂- 1 temp — assume same as il - 2 [ rickert , 2004 ] kfe_cd132_il7_cd127 = 0 ;% kre_cd132_il7_cd127 = 0 . 0138 ;% kf_cd132_il4_cd124 =( 1 /( na * veff )* kr_cd132_il4_cd124 / 4000 ;% 4 um [ zhang , 2003 ]— no on / off rates given kfe_cd132_il4_cd124 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd132_il4_cd124 = 0 . 0138 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_cd132_il15r_cd122 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_cd132_il15r_cd122 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_cd132_il15r_cd122 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd132_il15r_cd122 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kf_cd132_il15_il15r_cd122 =( 1 /( na * veff ))* 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kr_cd132_il15_il15r_cd122 = 0 . 0138 ;% min ̂- 1 , temp il - 2 [ fallon , 2000 ] kfe_cd132_il15_il15r_cd122 = 0 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] kre_cd132_il5il15r_cd122 = 0 . 0138 ;% temp leave as zero b / c “ neither population expressed il - 4ra and il - 15ra chains ” [ bielekova , 2006 ] in one embodiment , the method for assessing the provided values comprises the following equations : using our model , we determine the extent of signaling on various cytokine receptor types and examine the likelihood that each will reach a given threshold , based on the initial values provided above . the models enable us to address many unanswered questions . relevant to the question of response to anti - cd25 , we can quantitatively investigate whether blocking cd25 leads to the availability of more cd 132 for signaling from complexes between il - 7 and the il - 7 receptor . in one embodiment , the model is utilized to predict the effect of an anti - cd25 therapy on a subject prior to treatment . a first set of input values is provided , and the model is utilized to analyze the level of cytokine signaling prior to treatment . then , a second set of input values is utilized in which the number of available cd25 receptors is reduced to reflect the therapy &# 39 ; s effect , and the model is utilized to determine the level of signaling on various cytokine receptors after the administration of the therapy . in one embodiment , if il - 7 signaling increases significantly , then it is predicted that cd56bright nk cells will expand and the subject will respond to the therapy . for example , the modeling shows that for a subject represented by a certain set of input values , the quantity of cytokine will be the limiting factor in cytokine signaling . fig2 ( a ) shows an initial example , with concentrations of il - 2 , il - 7 , and il - 21 set to 0 . 1 nm each . in this case , the signaling plateaus occur when each cytokine runs out . when we provide a second set of values in which the amount of cd25 has been reduced to reflect the expected effect of the therapy , as shown in fig2 ( b ), there is little effect on the level of il - 7 or il - 21 signaling , because the concentration of cytokine and not the receptor levels remain the limiting factor . in one specific embodiment , this subject would be predicted to be a non - responder to anti - cd25 . in contrast , fig3 ( a ) shows the out put of the model for a different set of input values representing a different patient , in which the concentrations of il - 2 , il - 7 , and il - 21 are significantly higher at 10 nm each . in this case , when a second set of input values is provided with the levels of cd25 reduced to reflect the effect of an anti - cd25 therapy , as shown in fig3 ( b ), the level of il - 2 signaling drops as expected and the level of il - 7 signaling increases significantly . in one specific embodiment , this patient would be predicted to respond to an anti - cd25 therapy . predicting the effects of a baff antagonist on a subject prior to treatment in one embodiment , the therapy is a baff antagonist . the therapy &# 39 ; s target receptor subunits are baff - r , april , and taci . the ligands that interacts with the therapy &# 39 ; s target receptor subunits are baff and april . the receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are none . the ligands that interact with receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are none . the receptor subunits that interact with receptor subunits and ligands that bind to receptor subunits that interact with receptor subunits are none . a receptor subunit that binds to a ligand is hspg . in one embodiment , assaying a sample further comprises utilizing the following protocol adapted from [ cesana , 2006 ], [ venken , 2008 ], [ hatjiharissi , 2007 ] blood collection : whole blood is collected in heparin - containing vacutainer tubes ( bd or equivalent ). determining absolute cell counts : trucount tubes ( bd biosciences or equivalent ) are utilized to determine accurate cell counts . cells are stained with fluorescently labeled antibodies against the following maker ( human ). cd19 . b cell counts are determined using a facs aria or facs calibur ( bd biosciences or equivalent ). isolating peripheral blood mononuclear cells ( pbmcs ): pbmcs are isolated from whole blood using ficoll density gradient centrifugation ( histopaque , sigma - aldrich ; amersham ; or equivalent ). cell sorting : relevant subsets are separated . cells are stained with fluorescently labeled antibodies against the following marker ( human ). cd19 . the b cells are defined as : cd 19 + . b cells are isolated using a facs aria , facs calibur ( bd biosciences ) or equivalent . cell surface receptor quantification : the facs - sorted b cells collected above are stained with phycoerythrin ( pe ) conjugated antibodies against one or more of the following targets : baff - r , april , bcma , and hspg . one or more of the following reagents ( or equivalent ) is utilized : pe anti - human cd268 ( baff - r ) antibody ( catalog number 316905 , biolegend , san diego , calif . usa ) or pe mouse anti - human baff receptor ( catalog number 558097 becton dickinson biosciences , san jose , calif . usa ) polyclonal anti - human bcma / tnfrsf17 - phycoerythrin ( catalog number : fab193p , r & amp ; d systems , minneapolis , minn . usa ). monoclonal anti - human taci / tnfrsf13b / cd267 - phycoerythrin ( catalog number : fab1741p , r & amp ; d systems , minneapolis , minn . usa ) or pe rat anti - human cd267 ( catalog number 558414 becton dickinson biosciences , san jose , calif . usa ). intracellular and cell surface receptor quantification : after quantifying only the cell surface receptors using the above procedure , the cells can then be permeabilized using cytofix / cytoperm ( catalog number 554722 , becton dickinson biosciences , san jose , calif . usa ) or equivalent . then the above “ cell surface receptor quantification ” procedure can be repeated , but in this case will yield the total ( intracellular + cell surface ) receptor levels . the intracellular levels can then be calculated for each receptor by subtracting the surface levels from the total levels as in [ hodge , 2000 ]. measure cytokine levels : serum levels of baff and april can be determined using an elisa kit such as the quantikine human baff / blys / tnfsf13b immunoassay ( catalog number dblys0 , sblys0 , or pdblys , r & amp ; d systems , minneapolis , minn . usa ), and april human elisa kit ( catalog number khc3051 , invitrogen / life technologies , carlsbad calif . usa ). in one embodiment , the measurements resulting from the above protocols comprise the initial conditions that are input into the computational model as defined in the table below . in this example , cell type a is defined to be b cells , but in other embodiments it could be other cell types , or repeated for multiple cell types . note that br3 is the baff receptor . in one particular embodiment , the following format is used to define relevant parameters to represent interactions : kf_x_y is defined as the surface forward rate constant of x binding to y . kr_x_y is defined as the surface reverse rate constant of x binding to y . kfe_x_y is defined as the internal forward rate constant of x binding to y . kre_x_y is defined as the internal reverse rate constant of x binding to y . ksyn_x_y is defined as the rate at which x in synthesized in response to the binding event indicated in y . kt_celltypea_x is defined as the constitutive internalization rate of x on cell type a . ke_celltypea_x is defined as the internalization rate of x on cell type a . kh_celltypea_x is defined as the degradation rate of x on cell type a . kx_celltypea_x is defined as the recycling rate of x on cell type a . vs_celltypea_x is defined as the rate at which x is synthesized on cell type a . in one particular embodiment , using the above format to define parameters , the following parameters are provided from literature values as indicated , although in other embodiments other values may be used or the values may be measured : in one embodiment , the method for assessing the provided values comprises the following equations : in one embodiment , the therapy is a baff antagonist and the therapy &# 39 ; s expected effect is to reduce the concentration of baff in serum in one embodiment , these equations are solved with matlab in order to examine the effect of a baff antagonist on the competition between baff and april for binding to taci . this is relevant because the “ negative regulation is mediated via the baff : taci interaction , while positive effects ( e . g ., iga production , proliferation ) are transmitted via april : taci / hspg interactions .” [ salzer , 2007 ]. fig4 shows the output of such a model . fig4 ( a ) illustrates a first subject before ( left ) and after ( right ) treatment . the subject has lower initial april levels , so the baff antagonist will not be effective because even after the addition of the baff antagonist ( as represented by a reduction in baff concentration from 0 . 18 nm to 0 . 044 nm ), the negative signaling ( mediated by baff : taci ) still exceeds the positive signaling ( mediated by april : taci ). in contrast , the second subject ( illustrated in fig4 ( b )) has higher initial april levels before treatment ( left ), so the baff antagonist will be effective because after the addition of the baff antagonist ( as represented by a reduction in baff concentration from 0 . 18 nm to 0 . 044 nm ) ( right ), the negative signaling ( mediated by baff : taci ) no longer exceeds the positive signaling ( mediated by april : taci ). in one embodiment , the therapy is an inhibitor of a janus kinase ( jak ). in another embodiment , the therapy is specifically an inhibitor of jak3 . the therapy &# 39 ; s target receptor subunit is cd132 . the ligands that interacts with the therapy &# 39 ; s target receptor subunits are il - 2 , il - 4 , il - 7 , il - 9 , il - 15 , and il - 21 . the receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are cd25 , cd122 , cd124 , cd127 , cd129 , il - 15ralpha , and il - 21ralpha . the ligands that interact with receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are : il - 2 , il - 4 , il - 7 , il - 9 , il - 15 , and il - 21 . the receptor subunits that interact with receptor subunits and ligands that bind to receptor subunits that interact with receptor subunits are tslpr , il - 13ralpha1 , tslp , and il - 13 . a receptor subunit that binds to a ligand is il - 13ralpha2 . in one embodiment , the materials , methods , and model from example 1 are used to determine the extent of signaling caused by each cytokine . the effects of the therapy are predicted based on which gamma chain cytokine signals are present in a given subject . for instance , rheumatoid arthritis ( ra ) is believed to be mediated by th17 and / or th1 cells [ lubberts , 2010 ]. il - 21 is shown to increase the likelihood that naïve cd4 + t cells will develop into th17 cells , and consistent with the two aforementioned observations is the fact that il - 21 / il - 21r pathway blockade ameliorates disease in animal models of ra [ young , 2007 ]. on the other hand , il - 2 and il - 4 together increase the likelihood that naïve cd4 + t cells will develop in to th2 cells , and a transient rise in synovial fluid il - 2 and il - 4 levels in early ra [ raza , 2005 ]. we hypothesize that if the analysis described above determines that il - 21 signaling is the dominant gamma chain signaling in a given ra subject at a given time , then the jak3 inhibitor is likely to be effective because it will reduce the likelihood that naïve cd4 + t cells will become disease - producing th17 cells . on the other hand , if il - 2 and / or il - 4 is / are the dominant gamma chain signaling in a given ra subject at a given time , then the jak3 inhibitor is not likely to be effective because it will not reduce the likelihood that th17 or th1 cells will be generated . in one embodiment , the therapy comprises an antibody against interleukin - 5 ( il - 5 ). the therapy &# 39 ; s target receptor subunits are il - 5 receptor alpha and the common beta ( βc ) subunit . the ligand that interacts with the therapy &# 39 ; s target receptor subunits is il - 5 . the receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are gm - csf receptor alpha subunit and il - 3 receptor alpha subunit . the ligands that interact with receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are : gm - csf and il - 3 . in one embodiment , the concentration of gm - csf , il - 3 , and il - 5 are determined in serum using commercially available elisa kits . the surface and intracellular levels of il - 5 receptor alpha , gm - csf receptor alpha , il - 3 receptor alpha , and beta common are determined on one or more relevant cell types . in one embodiment , the relevant cell types include eosinophils . in another embodiment , the relevant cell type is eosinophils . in one embodiment , a computational model is then used to determine the effect of the anti - il - 5 in a given subject at a given time , taking into account not only its direct effect on il - 5 but also the effects on gm - csf and il - 3 signaling caused by the increased availability of beta common . in one embodiment , the therapy is a recombinant il - 21 . the therapy &# 39 ; s target receptor subunits are il - 21ralpha and cd132 . the ligands that interact with the therapy &# 39 ; s target receptor subunits are il - 21 . the receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are cd25 , cd122 , cd124 , cd127 , cd129 , and il - 15ralpha . the ligands that interact with receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are : il - 2 , il - 4 , il - 7 , il - 9 , il - 15 . the receptor subunits that interact with receptor subunits and ligands that bind to receptor subunits that interact with receptor subunits are tslpr , il - 13ralpha1 , tslp , and il - 13 . a receptor subunit that binds to a ligand is il - 13ralpha2 . in one embodiment , the materials , methods , and model from example 1 are used to determine the effect of il - 21 in a given patient at a given time , taking into account not only its direct effects but also the indirect effects caused by the decreased availability of cd132 . in one embodiment , the therapy is a recombinant il - 7 . the therapy &# 39 ; s target receptor subunits are cd 127 and cd 132 . the ligands that interacts with the therapy &# 39 ; s target receptor subunits are il - 7 . the receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are cd25 , cd122 , cd124 , cd129 , il - 15ralpha , and il - 21ralpha . the ligands that interact with receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are : il - 2 , il - 4 , il - 7 , il - 9 , il - 15 . the receptor subunits that interact with receptor subunits and ligands that bind to receptor subunits that interact with receptor subunits identified in are tslpr , il - 13ralpha1 , tslp , and il - 13 . a receptor subunit that binds to a ligand is il - 13ralpha2 . in one embodiment , the materials , methods , and model from example 1 are used to determine the effect of il - 7 in a given subject at a given time , taking into account not only its direct effects but also the indirect effects caused by the decreased availability of cd132 . in one embodiment , the therapy is a recombinant il - 15 . the therapy &# 39 ; s target receptor subunits are il - 15ralpha , cd122 , and cd132 . the ligands that interacts with the therapy &# 39 ; s target receptor subunits are il - 15 . the receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are cd25 , cd124 , cd127 , cd129 , and il - 21ralpha . the ligands that interact with receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are : il - 2 , il - 4 , il - 7 , il - 9 , il - 15 . the receptor subunits that interact with receptor subunits and ligands that bind to receptor subunits that interact with receptor subunits are tslpr , il - 13ralpha1 , tslp , and il - 13 . a receptor subunit that binds to a ligand is il - 13ralpha2 . in one embodiment , the materials , methods , and model from example 1 are used to determine the effect of il - 21 in a given patient at a given time , taking into account not only its direct effects but also the indirect effects caused by the decreased availability of cd132 . in one embodiment , the therapy comprises a recombinant gm - csf , such as sargramostim . the therapy &# 39 ; s target receptor subunits are gm - csf receptor alpha and the common beta ( βc ) subunit . the ligand that interacts with the therapy &# 39 ; s target receptor subunits is gm - csf . the receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are the il - 5 receptor alpha subunit and the il - 3 receptor alpha subunit . the ligands that interact with receptor subunits that interact with the therapy &# 39 ; s target receptor subunits are : il - 5 and il - 3 . in one embodiment , the concentration of gm - csf , il - 3 , and il - 5 are determined in serum using commercially available elisa kits . the surface and intracellular levels of il - 5 receptor alpha , gm - csf receptor alpha , il - 3 receptor alpha , and beta common are determined on one or more relevant cell types . in one embodiment , the relevant cell types include eosinophils . in another embodiment , the relevant cell type is eosinophils . in one embodiment , a computational model is then used to determine the effect of the gm - csf in a given patient at a given time , taking into account not only its direct effect but also the effects on il - 5 and il - 3 signaling caused by the decreased availability of beta common . in another embodiment , the effects of an anti - cd25 therapy on a given subject are predicted by determining the extent to which it makes additional il - 2 available to cd56bright nk cells . in subjects with tregs levels above a certain threshold , even the maximum dose of anti - cd25 may still leave a sufficient number of cd25 + tregs available to compete for il - 2 , such that cd56bright nk cells still will not be able to obtain enough il - 2 to reach their proliferation thresholds . in one embodiment , it is determined whether or not this is the case using measurements of treg levels , cd56bright nk cell levels , quantity of cd25 , cd122 , and cd132 on the tregs , quantity of cd25 , cd122 , and cd132 on the cd56bright nk cells , concentration of il - 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