Diagnostic method for distinguishing forms of esophageal eosinophilia
The invention provides methods for diagnosing eosinophilic esophagitis in a patient using a biomarker based assay directed to KCNJ2/Kir2.1 and related compositions, kits, and computer program products.
1. A method for diagnosing and treating eosinophilic esophagitis and proton pump inhibitor responsive esophageal eosinophilia (PPI-REE) in a patient in need of such diagnosis and treatment, the method comprising
a. receiving or obtaining an esophageal biopsy sample from the patient;
b. determining an expression level of a KCNJ2/Kir2.1 gene or gene product in the esophageal biopsy sample;
c. determining whether the expression level of the KCNJ2/Kir2.1 gene or gene product in the esophageal biopsy sample is above or below a threshold level;
d. diagnosing the patient as having eosinophilic esophagitis and administering a steroid to the patient having an expression level of the KCNJ2/Kir2.1 gene or gene product above the threshold level;
e. diagnosing the patient as having PPI-REE and administering a proton pump inhibitor to the patient having an expression level of the KCNJ2/Kir2.1 gene or gene product below the threshold level.
2. The method of claim 1 , wherein the method does not comprise a proton pump inhibitor (PPI) medication trial.
3. The method of claim 1 , wherein the patient has not been previously treated with a proton pump inhibitor.
4. The method of claim 1 , wherein the threshold level is relative to a reference expression level of the KCNJ2/Kir2.1 gene or gene product from normal esophageal tissue.
5. The method of claim 4 , wherein normal esophageal tissue is defined as having each of the following characteristics: normal endoscopic results, normal pathology with 0 eosinophils/ high power field, and no known history of eosinophilic esophagitis in the patient from whom the sample was obtained.
6. The method of claim 4 , wherein the reference is an average of a plurality of expression levels of the KCNJ2/Kir2.1 gene or gene product from a plurality of normal esophageal tissues.
7. The method of claim 1 , comprising the step of determining the expression level of the KCNJ2/Kir2.1 gene, wherein said gene expression is determined using a quantitative PCR-based method.
8. The method of claim 7 , wherein the expression level of the KCNJ2/Kir2.1gene is normalized.
9. The method of claim 8 , wherein the threshold level is 2 or 3-fold greater than a reference expression level of the KCNJ2/Kir2.1 gene from normal esophageal tissue.
10. The method of claim 7 , further comprising a step of extracting RNA from the esophageal biopsy sample.
11. The method of claim 10 , further comprising a step of converting the RNA to cDNA.
12. The method of claim 11 , further comprising a step of converting the cDNA into cRNA.
13. The method of claim 11 , wherein the cDNA or cRNA is labeled with a detectable marker.
14. The method of claim 13 , wherein the marker is biotin or a fluorescent molecule.
15. The method of claim 1 , comprising the step of determining the expression level of the KCNJ2/Kir2.1 gene product, wherein said gene product expression is determined using an immunostaining-based method, an antibody-based method, or a method comprising mass spectrophotometry.
16. The method of claim 15 , wherein the threshold level is 1.5-fold greater than a reference expression level of the KCNJ2/Kir2.1 gene product from normal esophageal tissue.
17. The method of claim 15 , wherein the threshold level is given in normalized units.
18. The method of claim 1 , wherein the method is performed in part using a computer program product, stored on a non-transitory computer readable medium, containing executable instructions that when executed cause a processor to perform operations comprising:
receiving the expression level of a KCNJ2/Kir2.1 gene or gene product in an esophageal biopsy sample obtained from a patient, and optionally, receiving a reference expression level of the KCNJ2/Kir2.1 gene or gene product from normal esophageal tissue;
receiving or calculating a threshold value;
comparing the KCNJ2/Kir2.1 gene or gene product expression level in the esophageal biopsy sample with the threshold value;
determining whether the KCNJ2/Kir2.1 gene or gene product expression level in the esophageal biopsy sample is above or below the threshold value;
outputting an indication of whether the KCNJ2/Kir2.1 gene or gene product expression level in the esophageal biopsy sample is above or below the threshold value.
19. The method of claim 18 , wherein the indication is a patient-specific report.
20. The method of claim 18 , wherein the report comprises a suggested diagnosis of eosinophilic esophagitis if the KCNJ2/Kir2.1 gene or gene product expression level in the esophageal biopsy sample is above the threshold value, or a suggested diagnosis of PPI-REE if the KCNJ2/Kir2.1 gene or gene product expression level in the esophageal biopsy sample is below the threshold value.