Patent Application
20070077585
1. Field of the Invention
The invention relates to an assay method for monitoring the biological response to IL-13 or IL-13 therapy using discovered biomarkers for IL-13.
2. Background and Related Art
Asthma is a complex, chronic disorder, with a genetic and an environmental component. It is characterized by reversible airway obstruction, airway hyper-responsiveness, airway inflammation and remodeling. Asthma affects an estimated 15 million Americans and the morbidity and mortality associated with it is on the rise in industrialized countries. 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 role of biomarkers is becoming increasingly important in the clinical development of therapeutics. A biomarker can be an indicator of normal biological processes, disease processes, or pharmacological responses to therapeutic intervention. 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.
The asthmatic population is very heterogeneous in terms of symptoms and response to therapy. Biomarkers can prove very useful in this by identifying responders versus non-responders. Thus leading to the development of more effective therapeutics.
This invention discloses the discovery of a panel of genes of which one or more can serve as biomarkers in an anti-interleukin(IL)-13 clinical trial.
The observation originated from data analysis of microarray gene expression profiling of peripheral blood mononuclear cells (PBMCs) from healthy donors. When comparing untreated PBMCs to PBMCs cultured with IL-13 or IL-4 this panel of genes was up regulated in all donors. The observation was confirmed by an independent method—Real Time Polymerase Chain Reaction (PCR) at messenger RNA level and the expression of all these 10 genes was up regulated by IL-13 and IL-4. A subsequent study looking at level of thymus and activation regulated chemokine (TARC) and macrophage derived chemokine (MDC) in the culture media supernatant of PBMCs showed that the neutralization of IL-13 by a fully human anti-interleukin 13 therapeutic antibody, as disclosed in US provisional patent application 60/679,925, filed May 11, 2005, published as U.S. Ser. No. ______, entirely incorporated herein by reference, inhibited the IL-13 induced TARC and MDC proteins as detected by ELISA. This disclosure presents evidence that this panel of genes can be used as biomarkers in an anti-IL-13 clinical study 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.
The panel of genes responsive to IL-13 disclosed provides methods for diagnosis or prognosis and tracking the efficacy of an anti-IL-13 therapy in IL-13 related disorders, including but not limited to, emphysema, asthma and chronic obstructive pulmonary disorder (COPD). Diagnostic and prognostic methods based on detecting these IL-13 responsive genes, or protein, in a sample is also disclosed.
Thus, in accordance with the invention, there is provided 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:
The present invention thus provides a new approach to monitoring anti-IL 13 therapy by detecting one or more biomarkers of IL-13, and IL-13 bioactivity. In summary, we have identified 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 are as disclosed herein. Such a 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.
The relevance of these genes to disease is very important for them to be effective biomarkers. To that end a number of the genes discussed above 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 [11], plasma of children during asthma exacerbation [12] and serum of patients with atopic dermatitis [13]. 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 cosinophil recruitment to the airways of asthmatics [14]. Also, CCL22 was shown to be up regulated in bronchoalveolar lavage (BAL) after a segmental allergen challenge of asthmatics[15].
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.
In one embodiment, the improvement is to use of at least one of WNT5A and MPIF-1 (CCL23) as a biomarker for IL-13 antagonist treatment or therapy.
Several methods have been reported for the measurement 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.
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.
Microarray Experiment Description:
Peripheral blood mononuclear cells (PBMCs) were isolated from 8 healthy donors. These were cultured in RPMI+10% FBS 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. Total RNA was isolated from the cells using the RNeasy kit (Qiagen). The quality and quantity of RNA was assessed using the bioanalyzer (Agilent) and microarray analysis was performed using the Affymatrix platform.
Number of samples: 40
Chip type: Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays were used in this study. 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.
Number of chips: 40
Data Processing and Analysis:
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 54675 probe sets on a chip, only 36357 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.
Microarray Resullts:
From the above analysis of the microarray data the following list of genes was identified as potential biomarkers for IL-13. These include:
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, did not modulate their expression. 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 finding 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 results are summarized in Table 2.
The Real Time PCR data seems to confirm the microarray data for each of the 10 genes.
Protein Analysis via ELISA:
To further confirm these data at the protein level a follow up study in PBMCs from 5 healthy donors was performed. PBMCs were cultured with IL-13 (10 ng/ml), IL-13 (10 ng/ml) plus anti-IL-13 therapeutic antibody, CNTO 607 (2 pg/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 3). These data suggest that TARC and MDC could serve as potential biomarkers in an anti-IL-13 clinical study.
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.
Here we describe the use of the Microarray technology platform to identify biomarkers that are associated with the biology of IL-13, which could prove useful in an anti-IL-13 clinical trial. Peripheral blood mononuclear cells (PBMCs) from 10 healthy donors were cultured in the presence of IL-13, IL-4, anti-IL-13 mAb or an isotype control mAb and RNA from the treated cells was subjected to microarray. This revealed a number of genes that showed increased expression in the IL-13 and IL-4 treatment groups e.g., CCL17 (TARC), CCL22 (MDC), CCL23 (MPIF-1) and CCL26 (Eotaxin 3). These results were confirmed by Real Time PCR. A follow up study in PBMCs from five healthy donors that were cultured with IL-1 3, IL-13 plus anti-IL-13 mAb or IL-13 plus isotype control mAb showed that the neutralization of IL-13 resulted in a down regulation of IL-13 induced TARC, MDC and eotaxin 3 at the protein level. These data suggest that TARC, MDC and eotaxin 3 could serve as a potential efficacy specific biomarkers in an anti-IL-13 clinical study.
Background
Asthma is a complex, chronic disorder, with a genetic and an environmental component (ST 1999). It is characterized by reversible airway obstruction, airway hyper-responsiveness, airway inflammation and remodeling (1997). Asthma affects an estimated 15 million Americans and the morbidity and mortality associated with it is on the rise in industrialized countries. 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 (Grunig G 1998; Wills-Karp M 1998; Walter D M 2001; Venkayya R 2002; Akbari O 2003) thus making it an attractive target for therapeutic intervention.
The role of biomarkers is becoming increasingly important in the clinical development of therapeutics. A biomarker can be an indicator of normal biological processes, disease processes, or pharmacological responses to therapeutic intervention (2001).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.
The asthmatic population is very heterogeneous in terms of symptoms and response to therapy. Biomarkers can prove very useful in this by identifying responders versus non-responders. Thus leading to the development of more effective therapeutics. One approach uses the DNA Microarray platform to identify biomarkers using precilinical models. Here we describe the use of the Microarray technology platform to identify biomarkers that are associated with the biology of IL-13, which could prove useful in an anti-IL-13 clinical trial.
Methods
Peripheral Blood Mononuclear Cell Isolation and Culture
Peripheral blood mononuclear cells (PBMCs) from healthy donors were isolated using Ficoll and density gradient centrifugation. The PBMCs were cultured in RPMI+10% FBS and left untreated or treated with IL-13 (10 ng/ml) or IL-4 (10 ng/ml) or anti-IL-13 mAb (10 μg/ml) or isotype control mAb (10 μg/ml ) for 24 hr.
RNA Isolation and Microarray
Total cellular RNA was isolated from the cells using the RNeasy mini kit (Qiagen, Inc. Valencia, Calif.) as per manufacturer's instructions. The IL-13 and IL-4 was purchased from R&D Systems (Minneapolis, Minn.). The quality and quantity of RNA was assessed using the Agilent 2100 Bioanalyzer (South Plainfield, N.J.). Samples that demonstrated high quality (ratio of 28S rRNA and 18S rRNA is greater than 1.7) were submitted for microarray analysis on the Affymatrix chip.
Microarray Processing
RNA amplification, probe synthesis and labeling, cDNA chip hybridization and washing were performed as described previously [17]. 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 54675 probe sets on a chip, only 36357 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, anti-IL-13 mAb, and isotype control mAb), 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.
Reverse Transcription and Real Time PCR
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 plolymerase (ABI biosystem, 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-Demand™ primers and probes (Applied Biosystems) were used in the PCR. The Real Time PCR data was analyzed using the standard curve method.
PBMC Culture and ELISA
PBMCs were cultured in the presence of IL-13 (10 ng/ml) or IL-13 (10 ng/ml)+anti-IL-13 mAb (10 μg/ml) or IL-13 (10 ng/ml)+isotype control mAb (10 μg/ml). Culture media supernatants were collected and tested for levels of TARC, MDC and eotaxin 3 protein at 24 hr and 48 hr time points using human TARC specific, MDC specific and human eotaxin 3 specific ELISA as per the manufacturer's instructions (R&D Systems)
Results
IL-13 Upregulates Genes in PBMCs
In order to identify genes downstream of IL-13, which could serve as potential efficacy specific biomarkers cDNA microarray technology platform was used. IL-4 was also included in the treatment groups to try and differentiate between IL-13 and IL-4 and identify any markers that could be uniquely regulated by IL-13 alone.
Ten donors were used and 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. From this a list of potential biomarkers was identified (Table 4).
Real Time PCR Validation
TaqMan™ Real Time PCR was used to validate the potential biomrkers. As shown in
Validation of Expression at Protein Level and Inhibition of IL-13 Induced Protein by an Anti-IL-13 mAb
In order to validate the modulation of genes by IL-13 at the protein level, ELISA was used to detect potein in cell culture supernatants and confirm upregulation of CCL17, CCL22 and CCL26 by IL-13. As shown in
Discussion
It is becoming increasing evident that there is a great need for biomarkers to become an integral part of drug discovery. Biomarkers can be especially valuable in helping to make early decisions on lead compounds and thereby drive down the cost of drug development. The microarray technology platform provides a unique approach in profiling the entire genome and thereby provide insight into potential markers that can help stratify a patient population or predict respone to therapy.
The asthmatic patient population is highly heterogenous both in terms of sysmptoms and response to therapy. Biomarkers can play a key role in identifying responders versus non-responders 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 signature genes.
Here we describe the use of microarray technology to identify genes associated with the biology of IL-13.We have identified a panel of potential biomarkers, associated with IL-13 biology, which are down regulated upon neutralizing IL-13 and thus can be useful in an anti-IL-13 clinical trial. Such a panel of biomarkers can be used as a tool to monitor the efficacy of an anti-IL-13 therapeutic antibody.
The relevance of these genes to disease is very important for them to be effective biomarkers. To that end a number of the genes discussed above 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 (T Sekiya 2002), plasma of children during asthma exacerbation (Leung, Wong et al. 2003) and serum of patients with atopic dermatitis (Hijnen, de Bruin-Weller et al. 2004). 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, Ohnona et al. 2001). Also, CCL22 was shown to be up regulated in bronchoalveolar lavage (BAL) after a segmental allergen challenge of asthmatics(Pilette, Francis et al. 2004). 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.
It is worth pointing out that he ultimate validity of a potential biomarker or panel of biomarkers can only be tested in the clinic. However, the purpose of this study and studies like this is to identify potential candidates which can be put forth for validation in a clinical setting.
Figure Legends:
This application claims priority to U.S. application No. 60/722,296, filed Sep. 30, 2005, which is incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 60722296 | Sep 2005 | US |
