{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T21:03:50Z","timestamp":1778015030628,"version":"3.51.4"},"reference-count":29,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2018,6,4]],"date-time":"2018-06-04T00:00:00Z","timestamp":1528070400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"name":"National Center for Advancing Translational Sciences of the National Institutes of Health","award":["UL1TR001067"],"award-info":[{"award-number":["UL1TR001067"]}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Aliment Pharmacol Ther"],"published-print":{"date-parts":[[2018,7]]},"abstract":"<jats:title>Summary<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Although current American guidelines distinguish proton pump inhibitor\u2010responsive oesophageal eosinophilia (PPI\u2010REE) from eosinophilic oesophagitis (EoE), these entities are broadly similar. While two microarray studies showed that they have similar transcriptomes, more extensive RNA sequencing studies have not been done previously.<\/jats:p><\/jats:sec><jats:sec><jats:title>Aim<\/jats:title><jats:p>To determine whether RNA sequencing identifies genetic markers distinguishing PPI\u2010REE from EoE.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We retrospectively examined 13 PPI\u2010REE and 14 EoE biopsies, matched for tissue eosinophil content, and 14 normal controls. Patients and controls were not PPI\u2010treated at the time of biopsy. We did RNA sequencing on formalin\u2010fixed, paraffin\u2010embedded tissue, with differential expression confirmation by quantitative polymerase chain reaction (PCR). We validated the use of formalin\u2010fixed, paraffin\u2010embedded vs RNAlater\u2010preserved tissue, and compared our formalin\u2010fixed, paraffin\u2010embedded EoE results to a prior EoE study.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>By RNA sequencing, no genes were differentially expressed between the EoE and PPI\u2010REE groups at the false discovery rate (FDR) \u22640.01 level. Compared to normal controls, 1996 genes were differentially expressed in the PPI\u2010REE group and 1306 genes in the EoE group. By less stringent criteria, only MAPK8IP2 was differentially expressed between PPI\u2010REE and EoE (FDR = 0.029, 2.2\u2010fold less in EoE than in PPI\u2010REE), with similar results by PCR. KCNJ2, which was differentially expressed in a prior study, was similar in the EoE and PPI\u2010REE groups by both RNA sequencing and real\u2010time PCR.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Eosinophilic oesophagitis and PPI\u2010REE have comparable transcriptomes, confirming that they are part of the same disease continuum.<\/jats:p><\/jats:sec>","DOI":"10.1111\/apt.14825","type":"journal-article","created":{"date-parts":[[2018,6,4]],"date-time":"2018-06-04T14:41:50Z","timestamp":1528123310000},"page":"219-225","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["RNA sequencing confirms similarities between PPI\u2010responsive oesophageal eosinophilia and eosinophilic oesophagitis"],"prefix":"10.1111","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1793-6027","authenticated-orcid":false,"given":"K. A.","family":"Peterson","sequence":"first","affiliation":[{"name":"Division of Gastroenterology University of Utah School of Medicine Salt Lake City UT USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Yoshigi","sequence":"additional","affiliation":[{"name":"Department of Pediatrics University of Utah School of Medicine Salt Lake City UT USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M. W.","family":"Hazel","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology University of Utah School of Medicine Salt Lake City UT USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D. A.","family":"Delker","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology University of Utah School of Medicine Salt Lake City UT USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E.","family":"Lin","sequence":"additional","affiliation":[{"name":"Human Genetics University of Utah School of Medicine Salt Lake City UT USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C.","family":"Krishnamurthy","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology University of Utah School of Medicine Salt Lake City UT USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"N.","family":"Consiglio","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics University of Utah School of Medicine Salt Lake City UT USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J.","family":"Robson","sequence":"additional","affiliation":[{"name":"Department of Pediatrics University of Utah School of Medicine Salt Lake City UT USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Yandell","sequence":"additional","affiliation":[{"name":"Human Genetics University of Utah School of Medicine Salt Lake City UT USA"},{"name":"USTAR Center for Genetic Discovery University of Utah School of Medicine Salt Lake City UT USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F.","family":"Clayton","sequence":"additional","affiliation":[{"name":"Department of Pathology University of Utah School of Medicine Salt Lake City UT USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2018,6,4]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1572-0241.2007.01179.x"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2011.02.040"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/ajg.2013.71"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cgh.2010.09.019"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1097\/MEG.0000000000000331"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1111\/apt.13141"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1111\/apt.12636"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/apt.12914"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/ajg.2013.363"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1097\/MPG.0b013e31819c4b3e"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2015-310991"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2015.07.008"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2015.07.033"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2012-302250"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0050037"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2014.08.043"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2016.11.028"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1097\/MPG.0000000000001019"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10620-009-0859-4"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1111\/apt.12513"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cgh.2014.02.037"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.2517-6161.1995.tb02031.x"},{"key":"e_1_2_7_24_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-15-419"},{"key":"e_1_2_7_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/gene.2014.27"},{"key":"e_1_2_7_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gie.2017.12.020"},{"key":"e_1_2_7_27_1","doi-asserted-by":"publisher","DOI":"10.1055\/s-0042-117274"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-323"},{"key":"e_1_2_7_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2014.12.1933"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2015.09.007"}],"container-title":["Alimentary Pharmacology &amp; Therapeutics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1111%2Fapt.14825","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/apt.14825","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,10]],"date-time":"2023-09-10T09:52:44Z","timestamp":1694339564000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/apt.14825"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,6,4]]},"references-count":29,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2018,7]]}},"alternative-id":["10.1111\/apt.14825"],"URL":"https:\/\/doi.org\/10.1111\/apt.14825","archive":["Portico"],"relation":{},"ISSN":["0269-2813","1365-2036"],"issn-type":[{"value":"0269-2813","type":"print"},{"value":"1365-2036","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,6,4]]},"assertion":[{"value":"2018-04-04","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-05-07","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-06-04","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}