# Patent

## Title
Compositions and methods for IL-13 biomarkers

## Abstract

Compositions and methods are provided for measuring and determining biomarkers for IL-13.

## Background
This application claims priority to U.S. application No. 60/722,296, filed Sep. 30, 2005, which is incorporated herein by reference.


BACKGROUND
The subject matter disclosed and claimed herein relates to methods for monitoring the biological response to IL-13 or IL-13 therapy using novel biomarkers for IL-13. This disclosure presents evidence that a panel of genes can be used as biomarkers in IL-13 studies for inflammatory disorders such as asthma, emphysema and chronic obstructive pulmonary disease (COPD), and may also play a role in other lung disorders with an inflammatory component. Of the panel of potential biomarkers described above, WNT5A and MPIF-1 (CCL23) have not been previously reported to be regulated by IL-13. These are novel IL-13 related biomarkers, which can be useful in any disease where IL-13 plays a major role.
Biomarkers can play a key role in identifying responders and non-responders to therapy and thereby lead to the development of more effective therapies. A number of studies have been described where microarray platform has been used to identify asthma and other inflammatory related signature genes.
The relevance of these genes to disease is very important for them to be effective biomarkers. To that end a number of the genes have been linked to diseases where IL-13 is believed to play a role. Increased level of TARC has been reported in serum and induced sputum of asthmatics (Sekiya, et al (2002), Allergy 57(2): 173-177.), plasma of children during asthma exacerbation (Leung et al., (2003), Eur. Respir J 21(4): 616-620.) and serum of patients with atopic dermatitis (Hijnen, et al., (2004), Journal of Allergy and Clinical Immunology 113(2): 334-340). This provides evidence that TARC might be involved in the pathogenesis of such disorders. Eotaxin 3 gene expression has been shown to be upregulated in bronchial biopsies of asthmatics after allergen challenge implying that Eotaxin 3 may be important in late-phase eosinophil recruitment to the airways of asthmatics (Berkman, et al. (2001), Am. J. Respir. Cell Mol. Biol. 24(6): 682-687). Also, CCL22 was shown to be up regulated in bronchoalveolar lavage (BAL) after a segmental allergen challenge of asthmatics (Pilette, et al. (2004), Eur Respir J 23(6): 876-884). Additionally, recent reports using murine models of allergic asthma have shown that the Th2 type cytokine IL-13 may play a critical role in the pathogenesis of asthma, either by regulating airway inflammation, mucus hyper-secretion or airway hyper-responsiveness thus making it an attractive target for therapeutic intervention.
The present invention provides a new approach to monitoring anti-IL13 therapy by detecting one or more biomarkers of IL-13, and IL-13 bioactivity. Described herein is a panel of potential biomarkers, associated with IL-13 biology, which can be useful in an anti-IL-13 clinical trial or for monitoring therapy using methods well known in the art. The panel of biomarkers can be used as a tool to monitor the efficacy of an anti-IL-13 therapeutic such as an IL-13 antagonist such as a small molecule or a biologic, and provide valuable information in terms of dosing amount and frequency.
SUMMARY OF THE INVENTION
Disclosed and claimed herein is the discovery of a panel of genes that can serve as biomarkers and may be useful in an anti-interleukin (IL)-13 trial.
The disclosed panel of genes responsive to IL-13 may be used in methods for diagnosing and tracking the efficacy of an anti-IL-13 therapy in IL-13 related disorders. These disorders include, but are not limited to, emphysema, asthma and chronic obstructive pulmonary disorder (COPD). Diagnostic and prognostic methods based on detecting and measuring expression of these IL-13 responsive genes, or protein, in a sample is also disclosed.
Specifically, described and claimed herein is a method of monitoring the response to anti-IL13 therapy in a patient undergoing such therapy by using one or more IL-13 biomarkers, which comprises: Determining the level of expression of at least one of WNT5A or MPIF-1 (CCL23) in a tissue sample of a patient; administering the anti-IL-13 therapy to the patient; measuring the level of at least one of WNT5A or MPIF-1 (CCL23) expression in said tissue of the patient and determining whether the anti-IL-13 therapy is effective in reducing the level of IL-13 or IL-13 related physiological effects.
The method can also include measuring at least one of the biomarkers CCL17 (TARC), CCL22 (MDC), CCL23 (MPIF-1) and CCL26 (Eotaxin 3), CD1A, CD1B, CD1C, IgE CD23A, IL-17Rbeta.
Several methods have been reported for the measurement of biomarker expression and any of these methods may be employed in the invention. These include (i) radioimmunoassays and single radial immunodiffusion procedures (Chambers, R. E. and Whicher, J. T. (1983); J. Immunol. Methods 59, 95; Marhaug, G. (1983) supra; Taktak, Y. S. and Lee, M. A. (1991); J. Immunol. Methods 136, 11); (ii) ELISA based assays (Zuckerman, S. H. and Suprenant, Y. M. (1986); J. Immunol. Methods 92, 3743; Dubois, D. Y. and Malmendier, C. L. (1988); J. Immunol. Methods 112, 71-75; Sipe, J. D. et al. (1989); J. Immunol. Methods 125, 125-135; Yamada, T. et al. (1989); Clin. Chim. Acta 179, 169-176; Tino-Casl, M. and Grubb, A. (1993); Arm. Clin. Biochem 30, 278-286); (iii) nephelometric methods (Vermeer, H. et al. (1990); Clin. Chem 36, 1192; Yamada, T. et al. (1993); Ann. Clin. Biochem. 30, 72-76); (iv) an electrophoretic procedure (Godenir, N. L. et al. (1985); J. Immunol. Methods 83, 217); (v) an immunochemiluminescence procedure (Hachem, H. et al. (1991); Clin. Biochem 24, 143-147); (vi) an automated method based on a monoclonal-polyclonal antibody solid phase enzymeimmunoassay (Wilkins, J. W. et al. (1994); Clin. Chem 40 (7), 1284-1290); and (vii) time-resolved fluorometric immunoassay (Malle, E., et al. (1995); J. Immunol. Methods 182, 131). See U.S. Pat. No. 6,194,163 which discloses a method for the quantitative measurement of human acute phase serum amyloid A protein.



DETAILED DESCRIPTION
Figure Descriptions
FIG. 1. Microarray data showing the average normalized intensity levels of CCL17, CCL22, CCL23 and CCL26 upon treatment of PBMCs from ten donors with IL-13, IL-4, anti-IL-13 mAb or isotype control mAb for 24 hrs.
FIG. 2. Real Time PCR (Taqman®) analysis showing the level of A) CCL17 B) CCL22C) CCL23 D) CCL26 upon treatment of PBMCs from ten donors with IL-13, IL-4, anti-IL-13 mAb or isotype control mAb for 24 hrs. The quantity of each gene is normalized to GAPDH.
FIG. 3. Effect of neutralizing IL-13. PBMCs were incubated with IL-13, IL-13+ anti-IL-13 mAb, or IL-13+ isotype control mAb for 24 hr and 48 hr timepoints. The level of A) CCL17 B) MDC C) CCL26 was assessed in the cell culture supernatants using ELISA.



The following experiments demonstrate that one or more of the biomarkers described herein can be used as accurate biomarker to monitor the response to anti-IL-13 therapies such as anti-IL-13 antibody therapy.
EXAMPLE 1
Microarray Experiment
Peripheral blood mononuclear cells (PBMCs) were isolated from 8 healthy donors using Ficoll and density gradient centrifugation. These were cultured in RPMI+10% FBS and left untreated or treated with IL-13 (10 ng/ml) or IL-4 (10 ng/ml) or an anti-IL-13 mAb (CNTO 607) (10 μg/ml) or human IgG1 isotype control (10 μg/ml) for 24 hrs. CNTO607 is described in U.S. provisional patent application 60/679,925, filed May 11, 2005, and published as WO/2006/124451, which are entirely incorporated herein by reference. The IL-13 and IL-4 was purchased from R&D Systems (Minneapolis, Minn.). Total cellular RNA was isolated from the cells using the RNeasy mini kit (Qiagen, Inc. Valencia, Calif.) as per manufacturer's instructions. Samples that demonstrated high quality (ratio of 28S rRNA and 18S rRNA is greater than 1.7) were submitted for microarray analysis on the Affymetrix chip.
Microarray Processing
RNA amplification, probe synthesis and labeling, cDNA chip hybridization and washing were performed using methods well known in the art. An Agilent Image Scanner was used to scan the cDNA chips (Agilent Technologies, Palo Alto, Calif.). Fluorescence intensity for each feature of the array was obtained by using ImaGene software (BioDiscovery, Los Angeles, Calif.).
Microarray Data Analysis
In this study, Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays were used to profile gene expression in human peripheral blood mononuclear cells from 10 donors stimulated with IL-13, or IL-4 at 1 time point (24 hr). Untreated samples from the same group of donors were used as control. Each array is comprised of more than 54K probe sets that analyze the expression level of over 47K transcripts and variants, including 38.5K well-characterized human genes. Raw intensity data was downloaded from DNA Chip III database. Values below 0.01 were set to 0.01. Using GeneSpring (Redwood City, Calif.; version 7.2), chip-to-chip normalization was performed by dividing the averaged intensity of each probe set by the median intensity of a chip. The intensity of each probe set was then normalized to the median intensity of that probe set in the control group. The control groups in this study were the 8 untreated samples.
A probe set was regarded as reliably detected if it was called “Present” or “Marginally Present” at least once among the 40 samples. Among 54,675 probe sets on a chip, only 36,357 probe sets passed the filtering and were analyzed further. Replicate samples were grouped according to their experimental conditions. The average of normalized intensities was used to represent each condition.
Using log 2 transformed normalized intensities, standard ANOVA was conducted in Partek Pro 6.1 (St. Charles, Mo.) to test treatment (untreated, IL13, IL4, CNTO 607, and isotype), and donor was also considered in the model as a random effect. Post-hoc tests were set up to identify genes showing significant differential expression between each treatment condition and untreated. False discovery rate cutoff was set at 0.05, meaning that 5% of identified genes would be false positives. Genes identified by statistical analysis were then filtered by fold change comparison between each treatment and untreated. The fold change cutoff was set at 1.5.







TABLE 1







The Raw And Normalized Intensities Of Each Of The Genes From


Microarray Analysis And Their Gen Bank Accession Numbers













Average
Average



Gene

Raw
Normalized
GenBank


(Probe set ID)
Treatment
Intensity
Intensity
Accession No.














CCL17
Untreated
138.8
1.086
NM_002987


(207900_at)







IL-13
2,268
17.62




IL-4
2,870
22.42




CNTO 607
130.8
1.005




Isotype
177.1
1.41




control





CCL26
Untreated
41
1.64
AF096296


(223710_at)







IL-13
1883
72.26




IL-4
1888
75.18




CNTO 607
41.02
1.51




Isotype
42.11
1.69




control





CCL23
Untreated
35.96
1.76
U58913


(210549_s_at)







IL-13
538.8
25.8




IL-4
674.8
33.8




CNTO 607
41.05
1.9




Isotype
120.1
6.2




control





CCL23
Untreated
17.8
1.4
U58913


(210548_at)







IL-13
268.1
21.2




IL-4
395.7
32.6




CNTO 607
25
2.0




Isotype
65.1
5.4




control





CCL22
Untreated
1550
1.2
NM_002990


(207861_at)







IL-13
4507
3.4




IL-4
4326
3.3




CNTO 607
1432
1




Isotype
2636
2




control





CD1A
Untreated
102.6
1
M28825


(210325_at)







IL-13
433.3
4.3




IL-4
586.6
6




CNTO 607
116.4
1.1




Isotype
93.4
0.9




control





CD1B
Untreated
104.7
1
NM_001764


(206749_at)







IL-13
1715
17.6




IL-4
2142
22.5




CNTO 607
92.9
0.9




Isotype
84.62
0.9




control





CD1C
Untreated
347.1
1
NM_001765


(205987_at)







IL-13
4251
12.79




IL-4
4864
15.01




CNTO 607
353
1




Isotype
289.8
0.9




control





WNT5A
Untreated
33.7
0.8
NM_003392


(205990_s_at)







IL-13
958.1
23.6




IL-4
1091
27.1




CNTO 607
40
0.9




Isotype
111.5
2.7




control





WNT5A
Untreated
32.1
1.4
NM_003392


(213425_at)







IL-13
390.6
17.6




IL-4
463.2
21




CNTO 607
31.6
1.4




Isotype
64.2
2.8




control





WNT5A
Untreated
35.8
1.7
NM_003392


(231227_at)







IL-13
248.8
11.7




IL-4
256.4
12.2




CNTO 607
20.9
1




Isotype
38
1.8




control





IgE CD23A
Untreated
106.8
1
NM_002002


(206759_at)







IL-13
2811
28.4




IL-4
3399
35.3




CNTO 607
99.5
1




Isotype
210.4
2.2




control





IgE CD23A
Untreated
58.4
1.4
NM_002002


(206760_s_at)







IL-13
2091
49.4




IL-4
2321
56.2




CNTO 607
27.2
0.6




Isotype
52.7
1.2




control





hIL-17 R beta
Untreated
83.2
2.3
NM_018725


(219255_x_at)







IL-13
379.7
10.3




IL-4
372.5
10.3




CNTO 607
122.7
3.3




Isotype
149.3
4.2




control





hIL-17 R beta
Untreated
123.9
1.1
NM_018725


(224156_x_at)







IL-13
447
4




IL-4
405.6
3.7




CNTO 607
153.2
1.3




Isotype
180.2
1.6




control





hIL-17 R beta
Untreated
100.9
1.2
NM_018725


(224361_s_at)







IL-13
362.9
4.5




IL-4
340.2
4.3




CNTO 607
128.3
1.6




Isotype
145.5
1.8




control









After analyzing the microarray data it became apparent that both IL-13 and IL-4 generated a very similar expression profile i.e., genes upregulated by IL-13 were the same as those upregulated by IL-4 at the 1.5 fold cutoff. All of these genes were up regulated with IL-4 and IL-13 when compared to untreated but CNTO 607 or isotype control, as shown in Table 1. From this data, a list of potential biomarkers was generated (Table 2). FIG. 2 shows a graphical representation of the microarray data for four of the biomarkers.







TABLE 2





Potential Biomarkers Associated With IL-13 Biology



















CCL17 (TARC thymus & activation regulated chemokine)




CCL26 (Eotaxin 3)




CCL23 (MPIF-1 myeloid progenitor inhibitory factor 1)




CCL22 (MDC macrophage derived chemokine)




CD1 A, B, C




WNT5A




IgE CD23A




hIL-17 R beta










For some of the genes more than one probe set was detected by microarray further confirming the results.
Real Time PCR (TaqMan) Confirmation:
In order to confirm the microarray findings by an independent means, Real Time PCR technology was employed. Total RNA from PBMCs cultured in the presence of IL-13 (10 ng/ml) or IL-4 (10 ng/ml) or CNTO 607 (10 μg/ml) or human IgG1 isotype control (10 μg/ml) for 24 hrs was reverse transcribed and used in Real Time PCR analysis for each of the 10 genes using the Applied Biosystems Gene Expression Assays on Demand on the ABI PRISM® 7900HT Sequence Detection System.
The Real Time PCR was conducted as follows. 1 μg of total RNA from each of the treated and untreated groups of PBMCs were used for the reverse transcription (RT) reaction. The RT reaction was performed as per protocol using TaqMan® RT reagents (Applied Biosystems) at 37° C. for 120 min followed by 25° C. for 10 min. Forty ng of cDNA per reaction were used in the Real Time PCR using the ABI Prism® 7900 sequence detection system (Foster City, Calif.). In the presence of AmpliTaq Gold DNA polymerase (ABI Biosystems, Foster City, Calif.), the reaction was incubated for 2 min at 50° C. followed by 10 min at 95° C. Then the reaction was run for 40 cycles at 15 sec, 95° C. and 1 min, 60° C. per cycle. Assays-on-DemandTM primers and probes (Applied Biosystems) were used in the PCR. The Real Time PCR data was analyzed using the standard curve method.







TABLE 3







The Mean RNA Quantity For Each Of The Genes At Various Treatment


Conditions Using Taqman












Mean RNA quantity





(Normalized to



Gene
Treatment
GAPDH)
Assay ID #













CCL17
Untreated
0.96
Hs00171074_ml



IL-13
289.6




IL-4
489




CNTO 607
0.96




Isotype
2.4




control




CCL26
Untreated
Undetected
Hs00171146_ml



IL-13
1.1




IL-4
1.3




CNTO 607
Undetected




Isotype
Undetected




control




CCL23
Untreated
0.57
Hs00270756_ml



IL-13
5.6




IL-4
6.3




CNTO 607
0.5




Isotype
1.24




control




CCL22
Untreated
1.4
Hs00171080_ml



IL-13
5.1




IL-4
5.1




CNTO 607
1.3




Isotype
2.4




control




CD1A
Untreated
1.1
Hs00233332_ml



IL-13
32.4




IL-4
42.5




CNTO 607
0.79




Isotype
1




control




CD1B
Untreated
1.3
Hs00233507_ml



IL-13
30.5




IL-4
38.4




CNTO 607
1.1




Isotype
1.4




control




CD1C
Untreated
0.9
Hs00233509_ml



IL-13
18.3




IL-4
19.8




CNTO 607
0.77




Isotype
0.5




control




WNT5A
Untreated
1.2
Hs00180103_ml



IL-13
147




IL-4
190.4




CNTO 607
2.1




Isotype
7.2




control




IgE CD23A
Untreated
0.79
Hs00233627_ml



IL-13
33.3




IL-4
35.8




CNTO 607
0.7




Isotype
1.4




control




hIL-17 R
Untreated
0.7
Hs00218889_ml


beta






IL-13
6




IL-4
5.8




CNTO 607
0.7




Isotype
1.1




control









As shown in Table 3, CCL17, CCL22, CCL23 and CCL26 were all upregulated by IL-13 or IL-4 while their expression was not modulated by anti-IL-13 mAb or the isotype control mAb. This is comparable to the microarray data set forth in Table 1.
EXAMPLE 2
In order to validate the modulation of genes by IL-13 at the protein level, ELISA was used to detect protein in cell culture supernatants and confirm upregulation of CCL17, CCL22 and CCL26 by IL-13. As shown in FIG. 3, IL-13 (10 ng/ml, 24 hr and 48 hr) stimulates the protein expression of CCL17, CCL22 and CCL26. Also neutralization of IL-13 by an anti-IL-13 mAb results in a down regulation of IL-13 induced CCL17, CCL22 and CCL26.
PBMC Culture and ELISA
PBMCs were cultured with IL-13 (10 ng/ml), IL-13 (10 ng/ml) plus anti-IL-13 therapeutic antibody, CNTO 607 (2 μg/ml) or IL-13 (10 ng/ml) plus isotype control mAb, human IgG1 (2 μg/ml) for 24 and 48 hr time points.
The PBMC culture supernatant was assayed for TARC protein using a human TARC ELISA assay (R&D Systems) and for MDC protein using a human MDC ELISA assay (R&D Systems). The data showed that the neutralization of IL-13 by CNTO 607 resulted in a down regulation of IL-13 induced TARC and MDC at the protein level (Table 4). These data suggest that TARC and MDC could serve as potential biomarkers in an anti-IL-13 clinical study.







TABLE 4







Mean Protein Level In PBMC Culture Supernatants From N = 5


Donors Following Various Treatment Conditions












TARC
MDC


Treatment
Time point
(pg/ml)
(pg/ml)













Untreated
24 hr
0.6
70.6


IL-13 (10 ng/ml)
24 hr
89
519.4


IL-13 (10 ng/ml) + human
24 hr
86.2
473.6


IgG1





(2 μg/ml)





IL-13 (10 ng/ml) + CNTO
24 hr
0.8
93.2


607





(2 μg/ml)





Untreated
48 hr
2
110


IL-13 (10 ng/ml)
48 hr
287
851.2


IL-13 (10 ng/ml) + human
48 hr
361.6
1398.2


IgG1





(2 μg/ml)





IL-13 (10 ng/ml) + CNTO
48 hr
2.4
240.2


607





(2 μg/ml)









The role of biomarkers is becoming increasingly important in the clinical development of therapeutics. Their role ranges from, stratifying the patient population in helping to identify responders versus non-responders, to determining the efficacy of the therapeutic. Biomarkers can be a valuable tool in making better decisions that will reduce the cost for drug development and enable therapies to reach the right patient population faster.

## Claims

1. A method for monitoring a response to IL-13 therapy in a patient undergoing IL13 therapy by measuring IL-13 associated-biomarker total RNA expression, comprising:
(a) in a first PBMC sample taken from a patient to be administered with IL-13 therapy, measuring the total RNA expression of a biomarker selected from the group consisting of WNT5A and MPIF-1(CCL23);
(b) administering IL-13 therapy to said patient;
(c) in a second PBMC sample taken from said patient after administering said IL-13 therapy, measuring the total RNA expression of a biomarker selected from the group consisting of WNT5A and MPIF-1 (CCL23); and
(d) comparing between the first and second PBMC samples, the level of biomarker total RNA expression, wherein said biomarker is selected from the group consisting of WNT5A and MPIF-1 (CCL23)
wherein a reduction in biomarker expression is indicative of a reduction in IL-13 activity following administering said IL-13 therapy.

2. The method of claim 1 wherein said IL-13 therapy is for the treatment of asthma, COPD or emphysema.

3. The method of claim 1 wherein the anti-IL-13 therapy is the administration of an anti-IL-13 antibody.

4. The method of claim 1, wherein said measuring of steps (a) and (c) further include the step of measuring the total RNA expression of a biomarker selected from the group consisting of: CCL17 (TARC), CCL22 (MDC), CCL23 (MPIF-1) and CCL26 (Eotaxin 3), CD1A, CD1B, CD1C, IgE CD23A, and IL-17Rbeta (GenBank Accession No. NM—018725).

5. The method of claim 1 wherein said biomarker is CCL23 (MPIF-1).

6. The method of claim 1 wherein said biomarker is WNT5A.