>MMP2|NM_001127891|3'UTR
   1 GCTGGCCCTGGCTCCCACAGGCCCTTCCTCTCCACTGCCTTCGATACACCGGGCCTGGAGAACTAGAGAAGGACCCGGAG
  81 GGGCCTGGCAGCCGTGCCTTCAGCTCTACAGCTAATCAGCATTCTCACTCCTACCTGGTAATTTAAGATTCCAGAGAGTG
 161 GCTCCTCCCGGTGCCCAAGAATAGATGCTGACTGTACTCCTCCCAGGCGCCCCTTCCCCCTCCAATCCCACCAACCCTCA
 241 GAGCCACCCCTAAAGAGATACTTTGATATTTTCAACGCAGCCCTGCTTTGGGCTGCCCTGGTGCTGCCACACTTCAGGCT
 321 CTTCTCCTTTCACAACCTTCTGTGGCTCACAGAACCCTTGGAGCCAATGGAGACTGTCTCAAGAGGGCACTGGTGGCCCG
 401 ACAGCCTGGCACAGGGCAGTGGGACAGGGCATGGCCAGGTGGCCACTCCAGACCCCTGGCTTTTCACTGCTGGCTGCCTT
 481 AGAACCTTTCTTACATTAGCAGTTTGCTTTGTATGCACTTTGTTTTTTTCTTTGGGTCTTGTTTTTTTTTTCCACTTAGA
 561 AATTGCATTTCCTGACAGAAGGACTCAGGTTGTCTGAAGTCACTGCACAGTGCATCTCAGCCCACATAGTGATGGTTCCC
 641 CTGTTCACTCTACTTAGCATGTCCCTACCGAGTCTCTTCTCCACTGGATGGAGGAAAACCAAGCCGTGGCTTCCCGCTCA
 721 GCCCTCCCTGCCCCTCCCTTCAACCATTCCCCATGGGAAATGTCAACAAGTATGAATAAAGACACCTACTGAGTGGCCGT
 801 GTTTGCCATCTGTTTTAGCAGAGCCTAGACAAGGGCCACAGACCCAGCCAGAAGCGGAAACTTAAAAAGTCCGAATCTCT
 881 GCTCCCTGCAGGGCACAGGTGATGGTGTCTGCTGGAAAGGTCAGAGCTTCCAAAGTAAACAGCAAGAGAACCTCAGGGAG
 961 AGTAAGCTCTAGTCCCTCTGTCCTGTAGAAAGAGCCCTGAAGAATCAGCAATTTTGTTGCTTTATTGTGGCATCTGTTCG
1041 AGGTTTGCTTCCTCTTTAAGTCTGTTTCTTCATTAGCAATCATATCAGTTTTAATGCTACTACTAACAATGAACAGTAAC
1121 AATAATATCCCCCTCAATTAATAGAGTGCTTTCTATGTGCAAGGCACTTTTCACGTGTCACCTATTTTAACCTTTCCAAC
1201 CACATAAATAAAAAAGGCCATTATTAGTTGAATCTTATTGATGAAGAGAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' agUCAAAGGAGACGUUUGUCaa 5' || |||| |:|||||| Target 5' agAGCTTCCAAAGTAAACAGca 3'	923 - 944	144.00	-12.30
2	miRNA 3' agUCAAAG----GA-GACG-------UUUGUCAa 5' |||||: || || | :|||||| Target 5' tcAGTTTTAATGCTACTACTAACAATGAACAGTa 3'	1085 - 1118	130.00	-12.31
3	miRNA 3' agucAAAGGAGACGUUUGUCAa 5' ||||:| : |:|||| Target 5' aaccTTTCTTACATTAGCAGTt 3'	483 - 504	110.00	-9.10

Mutant ID	Mutant Position	Mutant Source
887103	44	ClinVar
319770	52	ClinVar
887104	94	ClinVar
887105	112	ClinVar
319771	133	ClinVar
319772	160	ClinVar
319773	171	ClinVar
888371	184	ClinVar
319774	213	ClinVar
319775	229	ClinVar
888372	251	ClinVar
319776	261	ClinVar
888373	278	ClinVar
319777	401	ClinVar
319778	454	ClinVar
319779	499	ClinVar
885266	506	ClinVar
885267	524	ClinVar
319780	542	ClinVar
319781	628	ClinVar
885268	643	ClinVar
319782	670	ClinVar
886161	800	ClinVar
319783	854	ClinVar
319784	873	ClinVar
319785	931	ClinVar
886162	1013	ClinVar
886163	1030	ClinVar
886164	1049	ClinVar
319786	1063	ClinVar
319787	1205	ClinVar
887176	1205	ClinVar
COSN30106276	2	COSMIC
COSN30184265	9	COSMIC
COSN30187484	16	COSMIC
COSN30497500	16	COSMIC
COSN31508931	25	COSMIC
COSN31554863	43	COSMIC
COSN26984808	47	COSMIC
COSN31501613	49	COSMIC
COSN31555242	51	COSMIC
COSN13676487	52	COSMIC
COSN30694018	58	COSMIC
COSN31602003	61	COSMIC
COSN28869718	78	COSMIC
COSN30190985	82	COSMIC
COSN30188004	91	COSMIC
COSN31603676	95	COSMIC
COSN30177778	98	COSMIC
COSN31524237	103	COSMIC
COSN31560738	139	COSMIC
COSN31576920	249	COSMIC
COSN28753856	261	COSMIC
COSN21468763	424	COSMIC
COSN26648295	470	COSMIC
COSN7261079	502	COSMIC
COSN31520596	508	COSMIC
COSN28661609	542	COSMIC
COSN29534527	552	COSMIC
COSN25804902	651	COSMIC
COSN25304299	916	COSMIC
COSN32056276	1085	COSMIC
COSN24157724	1237	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs766093882	4	dbSNP
rs776631548	6	dbSNP
rs759388881	9	dbSNP
rs764880330	14	dbSNP
rs1324274455	19	dbSNP
rs964089006	24	dbSNP
rs752682273	33	dbSNP
rs368916369	35	dbSNP
rs369685795	43	dbSNP
rs751617004	44	dbSNP
rs757511901	45	dbSNP
rs781389911	46	dbSNP
rs746291867	48	dbSNP
rs1389948912	49	dbSNP
rs756516690	51	dbSNP
rs200211639	52	dbSNP
rs1422059945	57	dbSNP
rs1026962459	65	dbSNP
rs1315810930	67	dbSNP
rs1246994472	68	dbSNP
rs952803075	72	dbSNP
rs1466767564	77	dbSNP
rs760604174	77	dbSNP
rs1362297330	90	dbSNP
rs112159982	94	dbSNP
rs1319975418	95	dbSNP
rs563901621	95	dbSNP
rs1270603884	99	dbSNP
rs528402680	109	dbSNP
rs111489165	112	dbSNP
rs1275672282	120	dbSNP
rs961976369	125	dbSNP
rs55926431	133	dbSNP
rs1259293972	140	dbSNP
rs1446036097	144	dbSNP
rs1448145280	146	dbSNP
rs1356851662	148	dbSNP
rs1168771849	157	dbSNP
rs17860019	160	dbSNP
rs138597641	162	dbSNP
rs36115725	166	dbSNP
rs1180050078	167	dbSNP
rs947778867	169	dbSNP
rs1045236326	170	dbSNP
rs41280909	171	dbSNP
rs111371964	184	dbSNP
rs746687095	185	dbSNP
rs1452227533	188	dbSNP
rs773355464	193	dbSNP
rs1393930096	197	dbSNP
rs1052145936	200	dbSNP
rs1380785935	209	dbSNP
rs369694784	210	dbSNP
rs1156558619	212	dbSNP
rs147506379	213	dbSNP
rs776941141	218	dbSNP
rs1041202485	222	dbSNP
rs556071860	224	dbSNP
rs1337574857	226	dbSNP
rs886052126	229	dbSNP
rs1241049018	231	dbSNP
rs567900496	232	dbSNP
rs1450493146	234	dbSNP
rs1296973970	244	dbSNP
rs1441882827	249	dbSNP
rs746546784	250	dbSNP
rs776083935	251	dbSNP
rs7201	261	dbSNP
rs114011630	265	dbSNP
rs1259330584	274	dbSNP
rs1015600178	277	dbSNP
rs185162550	278	dbSNP
rs189316191	296	dbSNP
rs1799839	299	dbSNP
rs1259333685	305	dbSNP
rs557770088	311	dbSNP
rs1484812469	318	dbSNP
rs1279887708	322	dbSNP
rs1216518667	324	dbSNP
rs1318837460	337	dbSNP
rs180797471	338	dbSNP
rs1356720550	342	dbSNP
rs1295493403	346	dbSNP
rs540184171	356	dbSNP
rs1182416797	362	dbSNP
rs1374406432	369	dbSNP
rs1251205336	373	dbSNP
rs1298451054	375	dbSNP
rs1420798529	379	dbSNP
rs1454860269	384	dbSNP
rs1179463532	388	dbSNP
rs561637958	388	dbSNP
rs1157799549	397	dbSNP
rs1405871594	400	dbSNP
rs17860021	401	dbSNP
rs980659415	411	dbSNP
rs1474766435	414	dbSNP
rs1257017916	416	dbSNP
rs1187299791	426	dbSNP
rs369497688	434	dbSNP
rs1486999779	437	dbSNP
rs925020874	440	dbSNP
rs1177463537	448	dbSNP
rs562314074	454	dbSNP
rs1275609983	459	dbSNP
rs1468345231	474	dbSNP
rs1231787567	483	dbSNP
rs1336129205	494	dbSNP
rs1374781825	496	dbSNP
rs886052127	499	dbSNP
rs533480220	503	dbSNP
rs780960741	506	dbSNP
rs141779983	524	dbSNP
rs552111250	540	dbSNP
rs1368786329	542	dbSNP
rs1396525746	542	dbSNP
rs886052128	542	dbSNP
rs1305406580	544	dbSNP
rs1162733774	559	dbSNP
rs1799840	566	dbSNP
rs1460692752	568	dbSNP
rs760947188	571	dbSNP
rs1335579812	579	dbSNP
rs1409446962	590	dbSNP
rs1799818	595	dbSNP
rs186661803	597	dbSNP
rs1224450872	612	dbSNP
rs944245679	613	dbSNP
rs1430516682	617	dbSNP
rs17860023	621	dbSNP
rs886052129	628	dbSNP
rs1320928466	629	dbSNP
rs182135957	632	dbSNP
rs1468979835	636	dbSNP
rs900111888	642	dbSNP
rs771470902	643	dbSNP
rs1212335786	648	dbSNP
rs1048597641	660	dbSNP
rs17860024	670	dbSNP
rs571352875	671	dbSNP
rs1063976	675	dbSNP
rs1063977	677	dbSNP
rs1063978	680	dbSNP
rs1294427125	683	dbSNP
rs1015519826	687	dbSNP
rs1194014252	689	dbSNP
rs15142	690	dbSNP
rs895840362	695	dbSNP
rs1014233455	701	dbSNP
rs1058373	704	dbSNP
rs1024835623	706	dbSNP
rs969314564	707	dbSNP
rs980973810	717	dbSNP
rs1299601822	721	dbSNP
rs1460286591	722	dbSNP
rs1032182824	725	dbSNP
rs111803078	727	dbSNP
rs1170042812	732	dbSNP
rs1431774969	739	dbSNP
rs1396948599	742	dbSNP
rs1191894326	745	dbSNP
rs1468427270	746	dbSNP
rs1251879421	747	dbSNP
rs150600148	754	dbSNP
rs913675335	764	dbSNP
rs571732457	767	dbSNP
rs943669977	768	dbSNP
rs1234533051	783	dbSNP
rs866009096	785	dbSNP
rs976447594	799	dbSNP
rs112093666	800	dbSNP
rs868112480	801	dbSNP
rs1389417456	802	dbSNP
rs1296980365	809	dbSNP
rs932922938	810	dbSNP
rs1049009221	827	dbSNP
rs35646586	829	dbSNP
rs1435561636	830	dbSNP
rs888637547	836	dbSNP
rs539550309	854	dbSNP
rs775603988	855	dbSNP
rs895933919	856	dbSNP
rs373038333	857	dbSNP
rs753993450	865	dbSNP
rs1417897572	867	dbSNP
rs140455191	873	dbSNP
rs533551891	874	dbSNP
rs147262155	878	dbSNP
rs867091151	885	dbSNP
rs1308784513	888	dbSNP
rs1224553256	896	dbSNP
rs1277763888	898	dbSNP
rs1209464175	900	dbSNP
rs760876032	906	dbSNP
rs1350801537	907	dbSNP
rs1280820186	909	dbSNP
rs1236760956	910	dbSNP
rs1335163320	913	dbSNP
rs957875972	921	dbSNP
rs886052130	931	dbSNP
rs988406672	944	dbSNP
rs1357550152	948	dbSNP
rs575579593	953	dbSNP
rs1250742212	959	dbSNP
rs1020707310	962	dbSNP
rs1311317418	963	dbSNP
rs1413941472	964	dbSNP
rs1385722174	969	dbSNP
rs1490484651	970	dbSNP
rs1452255315	974	dbSNP
rs965165054	975	dbSNP
rs1266492955	976	dbSNP
rs1490108968	980	dbSNP
rs1476402204	983	dbSNP
rs1254907192	984	dbSNP
rs976377225	996	dbSNP
rs1186737829	1002	dbSNP
rs920941492	1009	dbSNP
rs1447267044	1013	dbSNP
rs1202925417	1014	dbSNP
rs763847728	1020	dbSNP
rs932870161	1033	dbSNP
rs764052225	1040	dbSNP
rs573620043	1041	dbSNP
rs1420432387	1042	dbSNP
rs910150010	1043	dbSNP
rs185917725	1048	dbSNP
rs776889997	1049	dbSNP
rs1037196323	1052	dbSNP
rs1168379520	1061	dbSNP
rs2052264	1063	dbSNP
rs1463509435	1068	dbSNP
rs950144654	1071	dbSNP
rs1163094534	1072	dbSNP
rs1475537367	1080	dbSNP
rs1044346008	1081	dbSNP
rs1425827999	1082	dbSNP
rs371723438	1082	dbSNP
rs1190328840	1083	dbSNP
rs1305425282	1085	dbSNP
rs1364103295	1086	dbSNP
rs905882150	1088	dbSNP
rs1404682106	1092	dbSNP
rs1289113410	1096	dbSNP
rs1332649522	1097	dbSNP
rs191126061	1098	dbSNP
rs1214945911	1100	dbSNP
rs1340249011	1117	dbSNP
rs1380067810	1122	dbSNP
rs1225282855	1129	dbSNP
rs1364502016	1130	dbSNP
rs1000626247	1131	dbSNP
rs1053693844	1133	dbSNP
rs1393005922	1148	dbSNP
rs1360146197	1150	dbSNP
rs1323233810	1155	dbSNP
rs1410896695	1165	dbSNP
rs765405697	1166	dbSNP
rs1165824256	1175	dbSNP
rs183272313	1176	dbSNP
rs750227380	1177	dbSNP
rs1289454815	1182	dbSNP
rs1195020600	1189	dbSNP
rs1009399648	1193	dbSNP
rs534203573	1199	dbSNP
rs758075499	1205	dbSNP
rs1283937268	1211	dbSNP
rs1270668285	1217	dbSNP
rs997950336	1221	dbSNP
rs1341788648	1223	dbSNP
rs1304246017	1224	dbSNP
rs1236596524	1227	dbSNP
rs1216210441	1231	dbSNP
rs1242954040	1239	dbSNP
rs1274803151	1243	dbSNP
rs1356610682	1250	dbSNP
rs1443339144	1250	dbSNP

- PloS one, 2012

Human alveolar macrophages are critical components of the innate immune system. Cigarette smoking-induced changes in alveolar macrophage gene expression are linked to reduced resistance to pulmonary infections and to the development of emphysema/COPD. We hypothesized that microRNAs (miRNAs) could control, in part, the unique messenger RNA (mRNA) expression profiles found in alveolar macrophages of cigarette smokers. Activation of macrophages with different stimuli in vitro leads to a diverse range of M1 (inflammatory) and M2 (anti-inflammatory) polarized phenotypes that are thought to mimic activated macrophages in distinct tissue environments. Microarray mRNA data indicated that smoking promoted an "inverse" M1 mRNA expression program, defined by decreased expression of M1-induced transcripts and increased expression of M1-repressed transcripts with few changes in M2-regulated transcripts. RT-PCR arrays identified altered expression of many miRNAs in alveolar macrophages of smokers and a decrease in global miRNA abundance. Stratification of human subjects suggested that the magnitude of the global decrease in miRNA abundance was associated with smoking history. We found that many of the miRNAs with reduced expression in alveolar macrophages of smokers were predicted to target mRNAs upregulated in alveolar macrophages of smokers. For example, miR-452 is predicted to target the transcript encoding MMP12, an important effector of smoking-related diseases. Experimental antagonism of miR-452 in differentiated monocytic cells resulted in increased expression of MMP12. The comprehensive mRNA and miRNA expression profiles described here provide insight into gene expression regulation that may underlie the adverse effects cigarette smoking has on alveolar macrophages.