Evaluation of eosinophilic esophagitis

This application is a Continuation in Part of U.S. application Ser. No. 11/721,127 filed Jun. 7, 2007, which claims priority from PCT/US2005/044456 filed Dec. 7, 2005, which claims priority from U.S. application Ser. No. 60/633,909 filed Dec. 7, 2004, each of which is expressly incorporated by reference herein in its entirety.

The U.S. Government has a paid-up license in this invention and the right in limited circumstances to require the patent owner to license others on reasonable terms as provided for by the terms of Grant No. 2R01AI045898-05 awarded by the National Institutes of Health.

The invention is directed generally to evaluating and mitigating eosinophilic esophagitis.

Patients with eosinophilic esophagitis may have symptoms that include abdominal pain, difficulty swallowing, vomiting, failure to thrive and weight loss. In addition, allergy, particularly food allergy, is an associated finding in most patients, and many have concomitant asthma or other chronic respiratory disease. Diagnosis requires endoscopy, and diseased tissue shows characteristic punctate white surface dots associated with erythema, loss of vascular pattern, ulcers, or ringed trachea-like appearance.

Patients with eosinophilic esophagitis typically have elevated levels of eosinophils in esophageal tissue and peripheral blood. Eosinophils are one type of granulocytic leukocyte (white blood cell) or granulocyte that normally appears in the peripheral blood at a concentration of about 1-3% of total leukocytes. Their presence in tissues is normally primarily restricted to the gastrointestinal mucosa, i.e. the stomach and intestines. Eosinophil accumulation in the peripheral blood and tissues is a hallmark feature of an allergic response, and may cause potent pro-inflammatory effects or tissue remodeling. Because eosinophilic esophagitis is marked by infiltration of eosinophils, this condition may be linked to allergen exposure. Eosinophil accumulation occurs in other allergic diseases such as allergic rhinitis, asthma, and eczema as well as parasitic infections, certain types of malignancies, chronic inflammatory disorders such as inflammatory bowel disease, specific syndromes such as eosinophilic gastroenteritis, eosinophilic colitis, eosinophilic cellulitis, eosinophilic fascitis, and systemic diseases such as Churg Strauss syndrome, eosinophilic pneumonia, and the idiopathic hypereosinophilic syndrome.

Numerous mediators have been identified as eosinophil chemoattractants. These include diverse molecules such as lipid mediators (platelet activating factor (PAF), leukotrienes) and chemokines such as the eotaxin subfamily of chemokines. Chemokines are small secreted proteins produced by tissue cells and leukocytes that regulate leukocyte homing during homeostatic and inflammatory states. Two main subfamilies (CXC and CC chemokines) are distinguished depending upon the arrangement of the first two cysteine amino acids, either separated by one amino acid (CXC), or adjacent (CC).

Due to the increasing incidence of eosinophilic esophagitis, methods to mitigate eosinophilic esophagitis would be beneficial. In addition, because eosinophilic esophagitis is often confused with other disorders such as gastroesophageal reflux disease (GERD), but does not typically respond to anti-GERD therapy, it is important to develop diagnostic features that distinguish between eosinophilic esophagitis and GERD. Diagnosis currently requires endoscopy with subsequent biopsy and analysis of the excised tissue by a pathologist based on manual microscopic analysis, so that less invasive methods of diagnosing eosinophilic esophagitis would also be beneficial.

The terms normal individuals, individuals without eosinophilic esophagitis (EE), control group or controls, patients without EE, and normal patients are used synonymously. The terms individuals with EE, treated groups, EE patients, and patients with EE are used synonymously.

One embodiment of the invention is a method of assessing eosinophilic esophagitis (EE) in a patient by comparing the patient\'s blood concentration of eotaxin-3 to a normal concentration of eotaxin-3, where an increased concentration of eotaxin-3 indicates EE.

Another embodiment of the invention is a diagnostic assay for EE. One embodiment of the assay may include a test strip containing an anti-eotaxin-3 antibody and at least one reagent that indicates binding of the anti-eotaxin-3 antibody to eotaxin-3 present in a supranormal level in a biological sample. Detection may be by visual inspection for a chromogen, fluorogen, colloidal gold agglutination, luminescence, etc.

Another embodiment of the invention is a diagnostic method for EE where eotaxin-3 DNA, eotaxin-3 mRNA, and/or eotaxin-3 protein is present over a normal amount in a patient tissue, as an indicator of EE in the patient.

Another embodiment of the invention is a diagnostic method for EE where a frequency of single nucleotide polymorphisms (SNPs) in the eotaxin-3 gene above normal frequency is an indicator of EE or a marker of disease risk, prognosis, and/or a response to therapy.

Another embodiment of the invention is a method to mitigate EE by providing an inhibitor to eotaxin-3 and/or a receptor, such as CCR3, for binding eotaxin-3 in a cell, such as a mast cell or an eosinophil, under conditions sufficient to inhibit eotaxin-3 binding to the receptor.

Another embodiment of the invention is a gene expression profile for EE comprising SEQ. ID NOS. 1-1620.

Another embodiment of the invention is a method to evaluate EE by gene expression profiles, where evaluation encompasses assessment of disease propensity, of disease severity, of therapy efficacy, of therapy compliance, etc. In one embodiment, EE is evaluated by determining an expression profile of at least one gene in the esophagus of the patient, where the gene is selected from SEQ ID NOS. 1-1620. In one embodiment, EE is evaluated by determining an expression profile of at least one gene in the patient, where the gene is selected from group consisting of SEQ ID NOS. 1-1620. The expression profile of the selected gene(s) is then compared to the expression profile of that same gene in an individual that does not have EE. The patient\'s propensity for EE is evaluated by determining if the gene in the patient is either over-expressed ≧1.5 times or is under-expressed ≧1.5 times compared to the same gene in the expression profile in the individual without EE. This propensity is evaluated by determining the extent that over-expression or under-expression exceeds 1.5, the identify of the gene over-expressed or under-expressed, and/or the number of genes that are over-expressed or under-expressed. The patient\'s propensity for EE is higher based on at least one of the farther the over-expression or under-expression is from 1.5, the gene is from SEQ ID NO. 1-42, and/or the greater the number of genes that are over-expressed or under-expressed. In one embodiment the gene is SEQ ID NO.1. In one embodiment, the patient lacks at least one clinical and/or physical symptoms of EE. In one embodiment, the cell is an esophageal cell.