ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgucUUCGU-AA-AGGUGUGUg 5' || || || |||||||| Target 5' ccccAACCACTTGTCCACACAg 3'	562 - 583	156.00	-11.60
2	miRNA 3' cgucuucgUAAAGGUGUGUg 5' || |||||||| Target 5' gaccaccgATGTCCACACAc 3'	542 - 561	152.00	-14.80
3	miRNA 3' cgUCUUCGUAAAGGUGUGUg 5' |||| |: ||||||| Target 5' acAGAAACG--GCCACACAt 3'	353 - 370	150.00	-19.30

Mutant ID	Mutant Position	Mutant Source
COSN28759659	16	COSMIC
COSN30460074	16	COSMIC
COSN8866998	32	COSMIC
COSN30542082	40	COSMIC
COSN23018917	45	COSMIC
COSN31566960	49	COSMIC
COSN1215784	54	COSMIC
COSN30459449	71	COSMIC
COSN30508480	77	COSMIC
COSN31517823	79	COSMIC
COSN30175672	82	COSMIC
COSN20042743	95	COSMIC
COSN13807010	114	COSMIC
COSN30576114	116	COSMIC
COSN28162184	122	COSMIC
COSN30664521	131	COSMIC
COSN32066950	142	COSMIC
COSN26972652	163	COSMIC
COSN30494652	188	COSMIC
COSN30151939	189	COSMIC
COSN30475007	230	COSMIC
COSN17077203	231	COSMIC
COSN507842	244	COSMIC
COSN30468443	271	COSMIC
COSN28187830	302	COSMIC
COSN24306699	341	COSMIC
COSN20044741	355	COSMIC
COSN30671859	387	COSMIC
COSN24610117	533	COSMIC
COSN20840576	572	COSMIC
COSN8552772	942	COSMIC
COSN17038068	1022	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1200684673	4	dbSNP
rs770053952	17	dbSNP
rs1451826833	19	dbSNP
rs1343969625	20	dbSNP
rs565005437	21	dbSNP
rs749360292	28	dbSNP
rs950804237	30	dbSNP
rs771178713	31	dbSNP
rs338583	32	dbSNP
rs1276037040	36	dbSNP
rs200780795	37	dbSNP
rs772265062	38	dbSNP
rs775924089	40	dbSNP
rs1339253685	42	dbSNP
rs1478530299	44	dbSNP
rs1193206194	47	dbSNP
rs554679420	49	dbSNP
rs1027271280	53	dbSNP
rs375475224	55	dbSNP
rs1169279045	56	dbSNP
rs750124972	58	dbSNP
rs982968826	59	dbSNP
rs762418146	60	dbSNP
rs1330313986	63	dbSNP
rs1436914745	67	dbSNP
rs765897139	69	dbSNP
rs751440912	70	dbSNP
rs1174121198	73	dbSNP
rs1227092734	79	dbSNP
rs754949487	81	dbSNP
rs368744339	88	dbSNP
rs752526789	91	dbSNP
rs1289780636	92	dbSNP
rs1340622276	93	dbSNP
rs755913782	94	dbSNP
rs1224201879	97	dbSNP
rs73931447	101	dbSNP
rs1449117962	102	dbSNP
rs1189411611	104	dbSNP
rs1392107056	106	dbSNP
rs749556490	114	dbSNP
rs771080858	115	dbSNP
rs1389917005	116	dbSNP
rs779144545	131	dbSNP
rs374775449	132	dbSNP
rs772625110	135	dbSNP
rs113139088	141	dbSNP
rs761077284	145	dbSNP
rs768941438	146	dbSNP
rs151058782	148	dbSNP
rs1284170468	149	dbSNP
rs762607311	151	dbSNP
rs545341311	152	dbSNP
rs117353963	154	dbSNP
rs759029586	155	dbSNP
rs752620409	157	dbSNP
rs1250118711	160	dbSNP
rs755903292	167	dbSNP
rs1186890178	171	dbSNP
rs763998925	172	dbSNP
rs200261766	176	dbSNP
rs1166955538	182	dbSNP
rs1409490231	184	dbSNP
rs779342891	188	dbSNP
rs549079599	189	dbSNP
rs1390349868	190	dbSNP
rs1171455563	192	dbSNP
rs758456211	194	dbSNP
rs1332959870	195	dbSNP
rs780578631	196	dbSNP
rs371056927	200	dbSNP
rs1380483151	201	dbSNP
rs747502390	202	dbSNP
rs1176175998	203	dbSNP
rs1328977352	205	dbSNP
rs1229390850	207	dbSNP
rs768952616	210	dbSNP
rs776986072	216	dbSNP
rs1200036496	218	dbSNP
rs748581103	227	dbSNP
rs770559766	230	dbSNP
rs774041118	231	dbSNP
rs1189994756	232	dbSNP
rs368537865	239	dbSNP
rs1249507309	244	dbSNP
rs1383342314	247	dbSNP
rs759057974	251	dbSNP
rs1159605146	260	dbSNP
rs1365279143	261	dbSNP
rs1464259541	268	dbSNP
rs766970740	269	dbSNP
rs1024276784	275	dbSNP
rs1209126122	280	dbSNP
rs775453658	288	dbSNP
rs894553684	292	dbSNP
rs1223329821	293	dbSNP
rs1001719664	294	dbSNP
rs1416076581	295	dbSNP
rs760538716	296	dbSNP
rs995532588	297	dbSNP
rs763910871	299	dbSNP
rs1410878546	300	dbSNP
rs757173760	304	dbSNP
rs1329669008	305	dbSNP
rs1232810155	306	dbSNP
rs561448837	311	dbSNP
rs531797176	313	dbSNP
rs887370599	314	dbSNP
rs1272456403	317	dbSNP
rs1482702674	319	dbSNP
rs532107319	321	dbSNP
rs750650298	323	dbSNP
rs1252413582	327	dbSNP
rs758463157	331	dbSNP
rs930245092	341	dbSNP
rs200083514	348	dbSNP
rs1360816764	349	dbSNP
rs1019783707	361	dbSNP
rs550002210	362	dbSNP
rs1416853342	364	dbSNP
rs1181867151	369	dbSNP
rs1325442263	369	dbSNP
rs1475838465	370	dbSNP
rs966447963	377	dbSNP
rs1257372478	386	dbSNP
rs965968265	387	dbSNP
rs1489456655	389	dbSNP
rs1438260510	395	dbSNP
rs763753574	396	dbSNP
rs911536254	403	dbSNP
rs1409370379	422	dbSNP
rs571510695	424	dbSNP
rs957764987	434	dbSNP
rs1174034117	445	dbSNP
rs1038997660	449	dbSNP
rs1408459050	450	dbSNP
rs1354800535	452	dbSNP
rs989122815	455	dbSNP
rs921836462	459	dbSNP
rs1330973534	460	dbSNP
rs1288014012	466	dbSNP
rs1374325058	468	dbSNP
rs930509510	484	dbSNP
rs1048846924	485	dbSNP
rs1164891507	488	dbSNP
rs10413194	490	dbSNP
rs886529953	494	dbSNP
rs538823592	496	dbSNP
rs796396708	508	dbSNP
rs1479039081	523	dbSNP
rs1262878375	528	dbSNP
rs879635126	529	dbSNP
rs1485031161	530	dbSNP
rs201831726	532	dbSNP
rs1392683968	540	dbSNP
rs8192798	549	dbSNP
rs115468544	550	dbSNP
rs1159308957	551	dbSNP
rs1271260866	552	dbSNP
rs1001479252	562	dbSNP
rs937873117	565	dbSNP
rs1307938321	576	dbSNP
rs1034598647	582	dbSNP
rs1380262590	586	dbSNP
rs957616560	592	dbSNP
rs1012162270	593	dbSNP
rs916017070	595	dbSNP
rs1020421821	596	dbSNP
rs80142449	597	dbSNP
rs977891913	602	dbSNP
rs554234896	603	dbSNP
rs139804572	605	dbSNP
rs1477979071	614	dbSNP
rs536702396	624	dbSNP
rs190828260	628	dbSNP
rs1200563245	630	dbSNP
rs1470359390	632	dbSNP
rs371166026	638	dbSNP
rs1028423217	639	dbSNP
rs577858484	642	dbSNP
rs1233122785	645	dbSNP
rs1010576089	646	dbSNP
rs10413449	647	dbSNP
rs907677812	655	dbSNP
rs940501322	662	dbSNP
rs1330352277	668	dbSNP
rs966386061	683	dbSNP
rs752274875	693	dbSNP
rs1045822452	707	dbSNP
rs981789195	709	dbSNP
rs1393452105	716	dbSNP
rs1184136344	721	dbSNP
rs1419716426	726	dbSNP
rs927896725	728	dbSNP
rs1434171096	730	dbSNP
rs1285150078	733	dbSNP
rs1484159697	736	dbSNP
rs907291365	737	dbSNP
rs1345541181	740	dbSNP
rs959297106	745	dbSNP
rs775196839	746	dbSNP
rs1275839622	748	dbSNP
rs539916376	752	dbSNP
rs1304166119	754	dbSNP
rs931388920	761	dbSNP
rs1196072410	764	dbSNP
rs1377757409	767	dbSNP
rs1313894586	768	dbSNP
rs1434466033	770	dbSNP
rs1055685039	772	dbSNP
rs1160507428	773	dbSNP
rs908620868	775	dbSNP
rs1274119999	777	dbSNP
rs1451430029	786	dbSNP
rs763512538	787	dbSNP
rs560861514	788	dbSNP
rs1011806339	792	dbSNP
rs572616106	794	dbSNP
rs903378307	797	dbSNP
rs1421652380	814	dbSNP
rs1349425860	815	dbSNP
rs1476501632	830	dbSNP
rs530219119	831	dbSNP
rs1389698519	839	dbSNP
rs1294411199	845	dbSNP
rs183019127	848	dbSNP
rs893934904	858	dbSNP
rs1018745222	861	dbSNP
rs1304817546	863	dbSNP
rs1382993156	869	dbSNP
rs1011025775	870	dbSNP
rs1020692106	873	dbSNP
rs1463056006	875	dbSNP
rs1418576643	877	dbSNP
rs561078531	884	dbSNP
rs531733556	893	dbSNP
rs796249464	896	dbSNP
rs974413049	897	dbSNP
rs1327728798	899	dbSNP
rs543971280	900	dbSNP
rs1446090786	902	dbSNP
rs952074814	906	dbSNP
rs1215066540	907	dbSNP
rs1334914024	909	dbSNP
rs1274413492	912	dbSNP
rs1034664546	919	dbSNP
rs959560396	923	dbSNP
rs984749308	928	dbSNP
rs565360931	930	dbSNP
rs75387715	931	dbSNP
rs547250262	934	dbSNP
rs920508557	935	dbSNP
rs1395334512	940	dbSNP
rs1325231305	941	dbSNP
rs940569143	942	dbSNP
rs779289921	944	dbSNP
rs928728486	949	dbSNP
rs1421512182	958	dbSNP
rs570226638	958	dbSNP
rs983269768	962	dbSNP
rs1055737345	971	dbSNP
rs1371051280	972	dbSNP
rs893158929	977	dbSNP
rs75334033	980	dbSNP
rs14477	981	dbSNP
rs894284530	982	dbSNP
rs977169925	983	dbSNP
rs773400564	984	dbSNP
rs1450413440	985	dbSNP
rs569359795	987	dbSNP
rs1008401939	992	dbSNP
rs1019759641	993	dbSNP
rs901605101	1000	dbSNP
rs1339127985	1002	dbSNP
rs1295790711	1011	dbSNP
rs1236779363	1013	dbSNP
rs566168718	1014	dbSNP
rs922593059	1015	dbSNP
rs1029142250	1016	dbSNP
rs1409215836	1020	dbSNP
rs757294461	1030	dbSNP
rs1394086460	1046	dbSNP
rs560733439	1047	dbSNP
rs527695009	1048	dbSNP

- PloS one, 2012

BACKGROUND: The characterization of miRNAs and their target mRNAs involved in regulation of the immune process is an area of intense research and relatively little is known governing these processes in allergic inflammation. Here we present novel findings defining the miRNA and mRNA transcriptome in eosinophilic esophagitis (EoE), an increasing recognized allergic disorder. METHODS: Esophageal epithelial miRNA and mRNA from five paired biopsies pre- and post-treatment with glucocorticosteroids were profiled using Taqman and Affymetrix arrays. Validation was performed on additional paired biopsies, untreated EoE specimens and normal controls. Differentially regulated miRNAs and mRNAs were generated, within which miRNA-mRNA target pairs with high predicted confidence were identified. RESULTS: Compared to the post-glucocorticoid treated esophageal mucosa, of all the 377 miRNA sequences examined, 32 miRNAs were significantly upregulated and four downregulated in the pre-treated biopsies. MiR-214 was the most upregulated (150 fold) and miR-146b-5b, 146a, 145, 142-3p and 21 were upregulated by at least 10 fold. Out of 12 miRNAs chosen for validation by qRT-PCR, five (miR-214, 146b-5p, 146a, 142-3p and 21) were confirmed and 11 shared the same trend. When the expression of the 12 miRNAs in the EoE mucosa was compared to unrelated normal mucosa, six (miR-214, 146b-5p, 146a, 21, 203, and 489) showed similar significant changes as in the paired samples and 10 of them shared the same trend. In the same five pairs of samples used to profile miRNA, 311 mRNAs were down-regulated and 35 were up-regulated in pre-treated EoE mucosa. Among them, 164 mRNAs were identified as potential targets of differentially regulated miRNAs. Further analysis revealed that immune-related genes, targeted and non-targeted by miRNAs, were among the most important genes involved in the pathogenesis of EoE. CONCLUSIONS: Our findings add to the accumulating body of data defining a regulatory role for miRNA in immune and allergic processes.