Method for diagnosing a molecular phenotype of a patient suffering from an illness accompanied by chronic inflammation

Abstract

Chronic inflammation is an increasing medical problem area of high socioeconomic significance. The invention relates to a method and a kit for diagnosing a molecular phenotype of a patient suffering from an illness accompanied by chronic inflammation, and to a medicament for treating such a patient. To that end, the gene expression of GATA-3 and/or Tbet in a biological isolate of the patient is measured and used for association with a molecular phenotype of the illness.

Claims

1. A method for diagnosing and treating chronic inflammation in a patient suffering from an illness associated with chronic inflammation, by identifying a molecular phenotype of the patient wherein the molecular phenotype is selected from the group consisting of the subgroups “Th2 high”, and “Th2 low” and the gene expression of Th2 cell-specific transcription factor (GATA-3) and/or the Th1 cell-specific transcription factor (Tbet) is measured in a biological isolate of the patient and used for the assignment to a molecular phenotype of the illness wherein the expression level of GATA-3 and/or Tbet is determined via the protein or mRNA quantity, and wherein the protein quantity is quantitatively determined by an immunoassay and wherein a therapeutic agent effective for specifically inhibiting GATA-3 or Tbet expression according to the identified molecular phenotype is administered to the patient.

2. The method according to claim 1, characterized in that the immunoassay is selected from the group consisting of an ELISA test, a radioimmunoassay, an electrochemiluminescence immunoassay, a CLIA (chemoluminescence-linked immunosorbent assay), an FLIA (fluorescence-linked immunosorbent assay) and a multiplex-assay.

3. The method according to claim 1, characterized in that an assignment of the patient to a molecular phenotype of the subgroup “Th2 high” occurs when at least one of the following conditions is fulfilled: the GATA-3gene expression in the biological isolate is higher than a defined reference value the ratio of GATA-3 : Tbet gene expression in the biological isolate is higher than a defined reference value.

4. The method according to claim 1, characterized in that an assignment of the patient to a molecular phenotype of the subgroup “Th2 low” occurs when at least one of the following conditions is fulfilled: the GATA-3 gene expression in the biological isolate is lower than a defined reference value, the ratio of GATA-3 : Tbet gene expression in the biological isolate is lower than a defined reference value.

5. The method according to claim 1, characterized in that along with the determination of the gene expression of GATA-3 and/or Tbet a determination of the serum IgE level and/or the number of eosinophilic granulocytes occurs and/or the Fe.sub.NO value is determined.

6. The method according to claim 1, characterized in that the illness accompanied by chronic inflammations is Th2-induced, such as for example allergic bronchial asthma, rhinoconjunctivitis, allergic sinusitis, atopical dermatitis, food allergies, pemphigus, ulcerative colitzis, parasitic illnesses, or Th1-induced, such as for example psoriasis, allergic contact eczema, Crohn's disease, COPD, rheumatoid arthritis, autoimmune diseases, type 1 diabetes mellitus or MS.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) Further features, details and advantages of the invention arise from the wording of the claims as well as from the following description of exemplary embodiments with the assistance of the drawings. The figures show the following:

(2) FIG. 1 shows the influence of various detergents on the release of GATA-3 from stimulated Jurkat cells,

(3) FIG. 2a,b show results of a quantification of Tbet and GATA-3 by means of chromogenic sandwich ELISA,

(4) FIG. 3 shows a standard curve of a GATA-3 ELISA for quantification of samples

(5) FIG. 4 shows a standard curve of a Tbet ELISA for quantification of samples

(6) FIG. 5 shows a standardized determination of Tbet in lysates of human peripheral mononuclear cells (PBMC)

(7) FIG. 6 shows a significant improvement of allergic airway inflammation after four-day treatment with the GATA-3 specific DNAzyme hgd40 (SEQ ID NO 40) compared to untreated mice,

(8) FIG. 7 shows the influence of the GATA-3 specific DNAzyme hgd40 (SEQ ID NO 40) on the number of neutrophils occurring in the chronic inflammation, the number of eosinophils in the BAL and the release of IL-5 after an eight-week treatment and

(9) FIG. 8 shows the influence of the GATA-3 specific DNAzyme hgd40 (SEQ ID NO 40) on the peribronchial/perivascular inflammation and goblet cell hyperplasia in the lung tissue.

DETAILED DESCRIPTION OF THE INVENTION

(10) Material and Methods:

(11) Cells can be isolated, for example, by means of technologies based on the binding of specific antibodies. Magnetic beads, which can be obtained from the firms Miltenyi (Macs-System), Dynal (DynaBeads) or BD-Bioscience (iMAG), are used. As an alternative this happens via a cell purification by means of fluorescent marked antibodies on cell sorters for example from the firm Cytomation (MOFLO) or BD-Bioscience (FACS-Vantage). The purity of the target cells is preferably at least 80%, more strongly preferred at least 95% and most preferred at least 99%.

(12) Methods for the isolation of RNA are e.g. described in Sambrook and Russell, Molecular Cloning, A Laboratory Manual, 3.sup.rd Edition, Cold Spring Harbor Laboratory (2001), New York and Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons (1998), New York. In addition it is possible for the average person skilled in the art to use commercially available kits (Silika-Technologie) e.g. the RNeasy Kit from the firm Qiagen, for RNA isolation. In addition it is preferable to purify mRNA directly from the target cells by using commercial kits for example from the firm Qiagen (Oligotex mRNA Kit), Promega (PolyATract mRNA Isolation System) or Miltenyi (mRNAdirect).

(13) Exemplary Embodiments

(14) Exemplary Embodiment 1

(15) GATA-3 and Tbet are proteins that, as transcription factors, have their effect in the cell core of T helper cells of the subtype Th1 and Th2. In order to determine the concentration of these two nuclear proteins in a specified volume of a biological isolate in particular in a specified volume of whole blood, cells which form GATA-3 and Tbet must first be isolated and subsequently lyzed. A direct proof of these proteins from human serum or plasma is not possible, since they are not present there in detectable concentration. An analysis of GATA-3 and Tbet therefore takes place in 4 stages: Partitioning and isolation of the GATA-3/Tbet expressing cells from the other cellular components of the whole blood Disruption of the cells and release of the intracellular/nuclear proteins Measurement of the concentration of GATA-3 and Tbet and Standardization of the found concentrations of GATA-3 and Tbet.
Partitioning and Isolation of the GATA-3/Tbet Expressing Cells from the Other Cellular Components of the Whole Blood

(16) This can be performed by different methods of variable complexity, in particular the following steps for partitioning and isolation within the scope of the present invention: An isolation of leukocytes from whole blood by means of Ficcoll density gradient centrifugation with subsequent affinity purification of the Th1/Th2 cell types by antibodies against specific surface markers, If necessary, the affinity purification of the Th1/Th2 cell types by antibodies against specific surface markers can also be performed as a 1-stage method without prior enrichment of the leukocytes, If necessary, the isolation of leukocytes through Ficoll density gradient centrifugation from whole blood suffices in order to perform a quantification of the proteins GATA-3 and Tbet, If necessary, in place of the Ficoll density gradient centrifugation a bead-based affinity purification of the Th1/Th2 cell types through antibodies against specific surface markers in a deep-well plate in the 96 well format can be employed, If required, in place of the Ficoll density gradient centrifugation a bead-based affinity purification of the leukocytes through antibodies against specific surface markers in a deep-well plate in the 96 well format can be employed, If necessary, a hypoosmolar lysis of the erythrocytes can take place to obtain a leukocyte preparation or If necessary the protein disruption can occur directly from the whole blood
Disruption of the Cells and Release of the Intracellular/Nuclear Proteins

(17) This can be achieved through various methods and principles, in particular within the scope of the present invention the following procedural steps: Destruction of cellular membranes through lysis buffers with different principles of operation: a) Hypotonic buffers which induce a bursting of the cells b) Buffers containing detergents, which destroy the cell membrane and as a result, release intracellular proteins c) Buffers of high ionic strength or osmotically active buffers which remove water from the cells and as a result destroy the cell integrity Physical methods such as heating up, shock freezing or ultrasound Mechanical methods such as homogenizing or grinding.

(18) Examples of buffers containing detergents could be: Buffer systems with a high concentration of ionic (e.g. SDS or cholate and its derivatives) or non-ionic (e.g. triton or Tween-20) detergents Mixtures of ionic and non-ionic detergents (e.g. Ripa buffers with 50 mM Tris.HCl (pH 7.5), 150 mM NaCl, 1% NP40, 0.5% sodium deoxycholate and 0.1% SDS) Commercially available lysis buffers with unknown composition (e.g. M-PER)
The influence of different detergents on the release of GATA-3 from stimulated Jurkat cells is illustrated in FIG. 1. The lysis of Jurkat cells (human T cell line) through various lysis buffers and quantification of GATA-3 by means of ELISA resulted in an especially high release of GATA-3 protein in the case of the use of the RIPA buffer (1% RIPA). About 50 ng/ml of GATA-3 were verified.
Measurement of the Concentration of GATA-3 and Tbet

(19) In principle, the concentration of the two transcription factors GATA-3 and Tbet can be determined with different methods. Within the scope of the present invention, among others there are: ELISA (enzyme linked immunosorbent assay) CLIA (chemoluminescence linked immunosorbent assay) FLIA (fluorescence linked immunosorbent assay) Mass spectrometric methods Chromatographic methods (e.g. gas chromatography) Fluid-based methods with solid phase separation, (e.g. HPLC) Microfluidic and nanofluidic methods

(20) FIG. 2a and FIG. 2b show the results of a quantification of Tbet and GATA-3 by means of chromogenic sandwich ELISA. The cells were obtained from whole blood through Ficoll density gradient centrifugation. The cells (stimulated human mononuclear cells) were lyzed with a Ripa buffer. The lysate was examined with two ELISA prototype methods with respect to the concentration of GATA-3 and Tbet. The concentration of the two proteins was depicted with respect to the total protein concentration of the cell lysates (standardization to protein content).

(21) The results in accordance with FIG. 2a show that Th1 cells have a higher content of Tbet (circa 160 ng/ml analyte/mg protein) than Th2 cells (circa 56 ng/ml analyte/mg protein) and this fact can be clearly confirmed from the results of the ELISA test:

(22) TABLE-US-00001 Ng/ml Tbet/mg Cells Protein Th2 B11-14 51.01 Th2 B11-15 58.40 Th2 B11-16 50.24 Th2 B11-17 68.79 Th2 B11-19 49.63 Th2 B11-20 55.85 Mean 55.65 STABW 7.31 VK (%) 13.14 Th1 B11-14 202.24 Th1 B11-19 106.34 Th1 B11-20 167.46 Mean 158.68 STABW 48.55 VK (%) 30.59

(23) The Tbet content in the Th1 cells is thus more than two times greater, namely by a factor of about three, than in the Th2 cells.

(24) According to FIG. 2b the content in GATA-3 in the Th2 cells (circa 10 ng/ml analyte/mg protein) is higher than in Th1 cells (circa 6 ng/ml analyte/mg protein) The GATA-3 content is more than 1.5 times higher in the Th2 cells here—namely by a factor of about 1.7—than in Th1 cells.

(25) In addition, one can see from FIGS. 2a and 2b that in the case of standardization to the protein content the quantity ratio of Tbet:GATA-3 in Th1 cells differs significantly form the corresponding ratio in Th2 cells. Thus the quantity ratio of Tbet:GATA-3 here in Th1 cells is about 27, thus more than 20, while the corresponding quantity ratio in Th2 cells is circa 6, thus less than 10.

(26) The quantitative determination of GATA-3 and Tbet occurs in each case by means of a sandwich ELISA (Enzyme linked immune sorbent assay).

(27) Exemplary Embodiment 2—GATA-3 ELISA:

(28) To this end, the wells of a 96 well microwell plate are coated with specific antibodies against GATA-3. After addition of the sample or of a standard, GATA-3 binds on the antibodies on the 96 well plate. After a wash step to remove the non-bound substances a second, specific biotinylated antibody against GATA-3 is added. After an additional wash step to remove the non-bound substances peroxidase marked streptavidin is added. After a last wash step to remove the non-bound substances substrate is added. The color development is terminated after a defined time by adding a stop solution. The intensity of the color development is quantified by a microwell plate reader. The quantification of the samples occurs by a comparison to the included standards of known protein concentration. FIG. 3 shows a corresponding standard curve of a GATA-3 ELISA.

(29) According to the exemplary embodiment for the performance of the GATA-3 ELISA, the steps relate to the following in detail: Insert number of required wells into a frame of the 96 well plate Addition of 50 μl/well assay buffer Addition of 100 μl/well standard/control/sample Incubation for 60 minutes on the shaker Wash all wells 4× with 400 μl/well of wash buffer Addition of 100 μl/well biotinylated anti-GATA-3 antibodies Incubation for 60 minutes on the shaker Wash all wells 4× with 400 μl/well of wash buffer Addition of 100 μl/well peroxidase marked streptavidin Incubation for 30 minutes on the shaker Wash all wells 4× with 400 μl/well of wash buffer Addition of 100 μl/well substrate Incubation for 30 minutes Stop reaction by addition of 100 μl stop solution Measurement of optical density at 450 nm with a microwell plate reader
Exemplary Embodiment 3—Tbet ELISA:

(30) The verification of the Tbet protein is executed in accordance with the following test principle: The quantitative determination of Tbet occurs by means of a sandwich ELISA (Enzyme linked immuno sorbent assay). To this end the wells of a 96 well microwell plate are coated with specific antibodies against Tbet. After addition of the sample or of a standard, Tbet binds on the antibodies on the 96 well plate. After a wash step to remove the non-bound substances a second, specific antibody against Tbet is added. After an additional wash step to remove the non-bound substances a peroxidase marked antibody against the Tbet specific antibody is added. After a last wash step to remove the non-bound substances substrate is added. The color development is terminated after a defined time by adding a stop solution. The intensity of the color development is quantified by a microwell plate reader. The quantification of the samples occurs by a comparison to the included standards of known protein concentration. FIG. 4 shows a corresponding standard curve of a Tbet ELISA.

(31) According to the exemplary embodiment for the performance of the Tbet ELISA the steps relate to the following in detail: Insert number of required wells into a frame of the 96 well plate Addition of 50 μl/well assay buffer Addition of 100 μl/well standard/control/sample Incubation for 60 minutes on the shaker Wash all wells 4× with 400 μl/well of wash buffer Addition of 100 μl/well anti-Tbet antibodies Incubation for 60 minutes on the shaker Wash all wells 4× with 400 μl/well of wash buffer Addition of 100 μl/well peroxidase marked anti-Tbet specific antibodies Incubation for 30 minutes on the shaker Wash all wells 4× with 400 μl/well of wash buffer Addition of 100 μl/well substrate Incubation for 30 minutes Stop reaction by addition of 100 μl stop solution Measurement of optical density at 450 nm with a microwell plate reader
Standardization of the Concentrations of GATA-3 and Tbet

(32) In order to consider differences in the sample preparation, a standardization of the concentrations of GATA-3 and Tbet can be performed. Differences in the sample preparation can arise e.g. due to the following: Differing cell numbers to be lyzed Differing lysis efficiencies of the individual samples or Differing content in the different cell types within the cell preparations.

(33) Possibilities for standardization include the following: Standardization to the total protein content of the cell lysate (see under “Measurement of the Concentrations of GATA-3 and Tbet”) Standardization to the cell number being lyzed (see FIG. 5) or Standardization to the concentration of specific marker proteins that are specifically found in specified cell types.

(34) FIG. 5 shows a standardized determination of Tbet in lysates of human peripheral mononuclear cells (PBMC). In the process a lysis of PBMCs of healthy subjects and patients suffering from allergic illnesses, such as e.g. allergic bronchial asthma, rhinoconjunctivitis, allergic sinusitis, atopical dermatitis, food allergies takes place. The concentration of Tbet was standardized to the cell number in the lysates. The illness is Th2 dependent and consistently a slight concentration in Tbet (circa 12 ng/ml/1 million cells) for allergy sufferers was determined compared to healthy subjects (circa 27 ng/ml/1 million cells). The Tbet concentration was thus reduced in the case of allergy sufferers by more than a factor of 2 compared to healthy subjects. Consequently, an assignment of the patients to the molecular phenotype “Th1 low” is easily possible here, since the Tbet gene expression in the biological isolate is lower than a defined reference value, here the Tbet gene expression of healthy subjects.

(35) Exemplary Embodiment 4

(36) In modification of Examples 2 and 3, in accordance with Example 4 Th1/Th2 cells are enriched by means of magnetic beads coated with cell specific antibodies for the sample preparation. Subsequently the verification of GATA-3 occurred in accordance with the provision according to Example 2.

(37) Exemplary Embodiment 5

(38) In modification of Examples 2 and 3, in accordance with Example 4 leukocytes are enriched by means of size exclusion filtration for the sample preparation. Subsequently the verification of GATA-3 occurred in accordance with the provision according to Example 2.

(39) Exemplary Embodiment 6

(40) A GATA-3 specific DNAzyme shows therapeutic effects in the mouse model of the OVA induced allergic airway inflammation of the “Th2 high” phenotype.

(41) In order to provide the best possible illustration of the clinical phenotype “Th2 high” in the mouse model BALB/c mice were sensitized with the model allergen ovalbumin (OVA) in the presence of the adjuvant AI(OH).sub.3 on days 0, 14 and 21 through intraperitoneal injection. On days 24-26 the mice inhaled a 1% OVA aerosol in order to cause a Th2 dominated allergic inflammatory reaction in the lungs. On days 23-26 the GATA-3 specific DNAzyme hgd40 (SEQ ID NO 40), dissolved in PBS, was intranasally administered. In the process the Balb/c-mouse strain is characterized in that it generates preferentially strong Th2 responses. This is reinforced by the use of AL(OH).sub.3 as an adjuvant, which distinctly supports the formation of Th2 dominated immune responses. The described mouse model is correspondingly characterized by a massive infiltration of eosinophils an Th2 cells in the airways accompanied by a hyperplasia of the mucus forming goblet cells with increased mucus production as well as the formation of an airway hyperresponsiveness. Immunologically, along with allergen specific Th2 cells, characterized by the production of the typical cytokines IL-4, IL-5 and IL-13, also OVA specific antibodies of the immune globulin classes IgE and IgG1 (in the mouse both Th2 dependent) were detectable. All these parameters are typical clinical features of a “Th2 high” phenotype (Wenzel et al., Am J Respir Crit Care Med. 199 September; 160(3):1001-8; Woodruff et al., 2009). In the process the reaction strength with respect to some parameters in the animal model were even more distinctly pronounced than in the clinical situation with human patients, e.g. eosinophilic granulocytes constitute circa 60-70% of all leukocytes in the bronchial alveolar lavage (BAL) in the mouse model, while already 3-5% of these cells in the sputum of patients indicates a Th2 dominated phenotype.

(42) According to FIG. 6, after four-day treatment with the GATA-3 specific DNYzyme hgd40 (SEQ ID NO 40) compared to untreated mice, a significant improvement of the allergic airway inflammation was ascertained. Above all the number of eosinophils in the BAL was significantly reduced. In addition, the BAL concentrations of the characteristic cytokines for the phenotype “Th2 high”, IL-5 and IL-13, were able to be significantly reduced.

(43) Exemplary Embodiment 7

(44) A GATA-3 specific DNAzyme shows significant therapeutic effects in the chronic mouse model of a Th2 dominated allergic airway inflammation.

(45) In order to provide the best possible illustration of the clinical phenotype “Th2 high” in the mouse model, BALB/c mice were sensitized with the model allergen ovalbumin (OVA) in the presence of the adjuvant AI(OH).sub.3 on days 0, 14 and 21 through intraperitoneal injection. By means of twice weekly OVA aerosol provocations over a time period of 14 weeks a chronic inflammation of the airways was caused in the mice. During the last eight weeks therapy was provided three times a week (until day 121) either with budesonide or the GATA-3 specific DNAzyme hdg40 through intranasal application.

(46) According to FIGS. 7 and 8 after eight weeks of treatment with GATA-3 specific DNAzyme hdg40 (SEQ ID NO 40) the number of eosinophils in the BAL was able to be significantly reduced and in addition a reduction of the number of neutrophils occurring in the chronic inflammation was also observed. This was accompanied by a lowered peribronchial/perivascular inflammation and reduced goblet cell hyperplasia. Simultaneously, in re-stimulated lymphocytes of those treated with hgd40 a reduced release of IL-5 was observed. In the budesonide group, on the other hand no significant improvement of the parameters cold be observed.

(47) The invention is not restricted to one of the previously described embodiments, but rather can be modified in many respects.

(48) All features and advantages arising from the claims, the description and the drawings, including design details, spatial arrangements and procedural steps can be essential to the invention both individually as well as in a variety of combinations.