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(12) Patent Application Publication (10) Pub. No.: US 2017/0067.111 A1 Rothenberg Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2017/0067.111 A1 Rothenberg Et Al US 20170067.111A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2017/0067.111 A1 Rothenberg et al. (43) Pub. Date: Mar. 9, 2017 (54) EVALUATION OF EOSINOPHILIC 2007, now Pat. No. 8,030.003, filed as application ESOPHAGITIS No. PCT/US2005/044456 on Dec. 7, 2005. (71) Applicant: CHILDRENS HOSPITAL (60) Provisional application No. 60/633,909, filed on Dec. MEDICAL CENTER, Cincinnati, OH 7, 2004. (US) Publication Classification (72) Inventors: Marc E. Rothenberg, Cincinnati, OH (51) Int. Cl. (US); Carrie Blanchard, Cincinnati, CI2O I/68 (2006.01) OH (US) A6II 3/56 (2006.01) (52) U.S. Cl. (21) Appl. No.: 15/340,282 CPC ............. CI2O 1/6883 (2013.01); A61 K3I/56 Filed: Nov. 1, 2016 (2013.01); C12O 2600/158 (2013.01); C12O (22) 2600/16 (2013.01) Related U.S. Application Data (57) ABSTRACT (63) Continuation of application No. 12/492.456, filed on Jun. 26, 2009, now abandoned, which is a continua A method to evaluate eosinophilic esophagitis based on tion of application No. 1 1/721,127, filed on Jun. 7, information in an eosinophilic esophagitis transcriptome. EE FO GENE SE GENEBANK SY-B NBER MBER N. EE RESPONDERS CHANGES PKB NMOO6952 C NMO280 SH2OB NMO53282 F NM000204 CA34.54 EM N-OOOO8707 AADAC2 NM2O7365 CH3 NMOO276 SNX 9 NMO 14758 AR NM000045 PNLFRF3 NMOOOO 709 SS - NM00942 Patent Application Publication Mar. 9, 2017. Sheet 1 of 4 US 2017/0067.111A1 18O, OO 60.00 40.00 2O, OO OC, OO 8O, OO 60.00 AO, OO 2O. OO OOO NORMA EE F. G. NORMAL GERO EE Patent Application Publication Mar. 9, 2017. Sheet 2 of 4 US 2017/0067.111A1 50 ditu/STIH8ONISOE ASP ASP SAINE W CCR3KO WT FIG. 3 FIG. 4 Patent Application Publication Mar. 9, 2017. Sheet 3 of 4 US 2017/0067.111A1 (Xn1338)38NMOU 333A11JWNINM00 830N0dS38NON 830N0dS38 d3+1310 830N0&S38NON 083 Patent Application Publication Mar. 9, 2017. Sheet 4 of 4 US 2017/0067.111 A1 296900WN 019120WN S98102WN 90792IXW 91.2100WN 891;10WN Sy(0000WN 601100100WN 276100WN 0103S (38WTIN 3N39 T08WAS 92H00 8102HS 31 !TEIHO 61XNS 1987 €dddITNd 9•IJ 0703 S39NWHO 33 US 2017/OO671 11 A1 Mar. 9, 2017 EVALUATION OF EOSINOPHILC 0007 Due to the increasing incidence of eosinophilic ESOPHAGITIS esophagitis, methods to mitigate eosinophilic esophagitis would be beneficial. In addition, because eosinophilic RELATED APPLICATION esophagitis is often confused with other disorders such as 0001. This is a Continuation of U.S. application Ser. No. gastroesophageal reflux disease (GERD), but does not typi 12/492,456 filed Jun. 26, 2009, which is a Continuation in cally respond to anti-GERD therapy, it is important to Part of U.S. application Ser. No. 1 1/721,127 filed Jun. 7, develop diagnostic features that distinguish between eosino 2007, now U.S. Pat. No. 8,030,003 granted Oct. 4, 2011, philic esophagitis and GERD. Diagnosis currently requires which claims priority from PCT/US2005/044456 filed Dec. endoscopy with Subsequent biopsy and analysis of the 7, 2005, which claims priority from U.S. application Ser. excised tissue by a pathologist based on manual microscopic No. 60/633,909 filed Dec. 7, 2004, each of which is analysis, so that less invasive methods of diagnosing eosino expressly incorporated by reference herein in its entirety. philic esophagitis would also be beneficial. 0002. This invention was made with U.S. Government SUMMARY OF THE INVENTION support on behalf of Grant No. 2R01A1045898-05 awarded by the National Institutes of Health. The U.S. Government 0008. The terms normal individuals, individuals without has certain rights in this invention. eosinophilic esophagitis (EE), control group or controls, patients without EE, and normal patients are used synony FIELD OF THE INVENTION mously. The terms individuals with EE, treated groups, EE patients, and patients with EE are used synonymously. 0003. The invention is directed generally to evaluating 0009. One embodiment of the invention is a method of and mitigating eosinophilic esophagitis. assessing eosinophilic esophagitis (EE) in a patient by comparing the patients blood concentration of eotaxin-3 to BACKGROUND a normal concentration of eotaxin-3, where an increased 0004 Patients with eosinophilic esophagitis may have concentration of eotaxin-3 indicates EE. symptoms that include abdominal pain, difficulty Swallow 0010. Another embodiment of the invention is a diagnos ing, vomiting, failure to thrive and weight loss. In addition, tic assay for EE. One embodiment of the assay may include allergy, particularly food allergy, is an associated finding in a test strip containing an anti-eotaxin-3 antibody and at least most patients, and many have concomitant asthma or other one reagent that indicates binding of the anti-eotaxin-3 chronic respiratory disease. Diagnosis requires endoscopy, antibody to eotaxin-3 present in a Supranormal level in a and diseased tissue shows characteristic punctuate white biological sample. Detection may be by visual inspection for Surface dots associated with erythema, loss of vascular a chromogen, fluorogen, colloidal gold agglutination, lumi pattern, ulcers, or ringed trachea-like appearance. neScence, etc. 0005 Patients with eosinophilic esophagitis typically 0011. Another embodiment of the invention is a diagnos have elevated levels of eosinophils in esophageal tissue and tic method for EE where eotaxin-3 DNA, eotaxin-3 mRNA, peripheral blood. Eosinophils are one type of granulocytic and/or eotaxin-3 protein is present over a normal amount in leukocyte (white blood cell) or granulocyte that normally a patient tissue, as an indicator of EE in the patient. appears in the peripheral blood at a concentration of about 0012 Another embodiment of the invention is a diagnos 1-3% of total leukocytes. Their presence in tissues is nor tic method for EE where a frequency of single nucleotide mally primarily restricted to the gastrointestinal mucosa, i.e. polymorphisms (SNPs) in the eotaxin-3 gene above normal the stomach and intestines. Eosinophil accumulation in the frequency is an indicator of EE or a marker of disease risk, peripheral blood and tissues is a hallmark feature of an prognosis, and/or a response to therapy. allergic response, and may cause potent pro-inflammatory 0013 Another embodiment of the invention is a method effects or tissue remodeling. Because eosinophilic esoph to mitigate EE by providing an inhibitor to eotaxin-3 and/or agitis is marked by infiltration of eosinophils, this condition a receptor, such as CCR3, for binding eotaxin-3 in a cell, may be linked to allergen exposure. Eosinophil accumula Such as a mast cell or an eosinophil, under conditions tion occurs in other allergic diseases such as allergic rhinitis, sufficient to inhibit eotaxin-3 binding to the receptor. asthma, and eczema as well as parasitic infections, certain 0014) Another embodiment of the invention is a gene types of malignancies, chronic inflammatory disorders such expression profile for EE comprising SEQ. ID NOS. 1-1620. as inflammatory bowel disease, specific syndromes such as 0015. Another embodiment of the invention is a method eosinophilic gastroenteritis, eosinophilic colitis, eosino to evaluate EE by gene expression profiles, where evaluation philic cellulitis, eosinophilic fasciitis, and systemic diseases encompasses assessment of disease propensity, of disease Such as Churg Strauss syndrome, eosinophilic pneumonia, severity, of therapy efficacy, of therapy compliance, etc. In and the idiopathic hypereosinophilic syndrome. one embodiment, EE is evaluated by determining an expres 0006 Numerous mediators have been identified as sion profile of at least one gene in the esophagus of the eosinophil chemoattractants. These include diverse mol patient, where the gene is selected from SEQ ID NOS. ecules such as lipid mediators (platelet activating factor 1-1620. In one embodiment, EE is evaluated by determining (PAF), leukotrienes) and chemokines such as the eotaxin an expression profile of at least one gene in the patient, subfamily of chemokines. Chemokines are small secreted where the gene is selected from group consisting of SEQID proteins produced by tissue cells and leukocytes that regu NOS. 1-1620. The expression profile of the selected gene(s) late leukocyte homing during homeostatic and inflammatory is then compared to the expression profile of that same gene states. Two main subfamilies (CXC and CC chemokines) are in an individual that does not have EE. The patients distinguished depending upon the arrangement of the first propensity for EE is evaluated by determining if the gene in two cysteine amino acids, either separated by one amino the patient is either over-expressed 1.5 times or is under acid (CXC), or adjacent (CC). expressed 1.5 times compared to the same gene in the US 2017/OO671 11 A1 Mar. 9, 2017 expression profile in the individual without EE. This pro of an individual prescribed therapy for EE is compared to an pensity is evaluated by determining the extent that over expression profile of the same gene(s) from an individual expression or under-expression exceeds 1.5, the identify of without EE. The individuals compliance with therapy is the gene over-expressed or under-expressed, and/or the evaluated by determining if the at least one gene is either number of genes that are over-expressed or under-expressed. over-expressed 1.5 times or is under-expressed 1.5 times The patient’s propensity for EE is higher based on at least compared to the same gene in the expression profile from the one of the farther the over-expression or under-expression is individual without EE. The individuals compliance with from 1.5, the gene is from SEQ ID NO. 1-42, and/or the therapy is determined based on the extent that over-expres greater the number of genes that are over-expressed or sion or under-expression exceeds 1.5, the identify of the under-expressed.
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