;PMID: 10220498 ;source_file_1302.mrg ;Release 0.9 of PennBioIE ;Funded by NSF ITR EIA-0205448 ;0)section:[e:0..41] = [t:0..41] ;1)sentence:[e:46..120] = [t:46..120] ;2)section:[e:124..158] = [t:124..158] ;3)section:[e:162..257] = [t:162..257] ;4)sentence:[e:261..279] = [t:261..279] ;5)sentence:[e:280..338] = [t:280..338] ;6)sentence:[e:340..437] = [t:340..437] ;7)sentence:[e:438..575] = [t:438..575] ;8)sentence:[e:577..585] = [t:577..585] ;9)sentence:[e:586..693] = [t:586..693] ;10)sentence:[e:694..762] = [t:694..762] ;11)sentence:[e:763..876] = [t:763..876] ;12)sentence:[e:877..935] = [t:877..935] ;13)sentence:[e:936..1001] = [t:936..1001] ;14)sentence:[e:1002..1141] = [t:1002..1141] ;15)sentence:[e:1142..1150] = [t:1142..1150] ;16)sentence:[e:1151..1321] = [t:1151..1321] ;17)sentence:[e:1322..1421] = [t:1322..1421] ;18)sentence:[e:1422..1506] = [t:1422..1506] ;19)sentence:[e:1507..1622] = [t:1507..1622] ;20)sentence:[e:1623..1782] = [t:1623..1782] ;21)sentence:[e:1783..1986] = [t:1783..1986] ;22)sentence:[e:1988..2000] = [t:1988..2000] ;23)sentence:[e:2001..2121] = [t:2001..2121] ;24)section:[e:2125..2170] = [t:2125..2170] ;section 0 Span:0..41 ;Gastroenterology 1999 May;116(5):1063-71 (SEC (FRAG (IN:[0..16] Gastroenterology) (CD:[18..22] 1999) (NNP:[23..26] May) (CD:[26..30] ;116) (-LRB-:[30..31] -LRB-) (CD:[31..32] 5) (-RRB-:[32..33] -RRB-) (::[33..34] :) (CD:[34..38] 1063) (::[38..39] -) (CD:[39..41] 71))) ;sentence 1 Span:46..120 ;Association of K-ras mutations with p16 methylation in human colon cancer. ;[61..66]:gene-rna:"K-ras" ;[82..85]:gene-rna:"p16" ;[107..119]:malignancy-type:"colon cancer" (SENT (NP-HLN (NP (NN:[46..57] Association)) (PP (IN:[58..60] of) (NP (NN:[61..66] K-ras) (NNS:[67..76] mutations))) (PP (IN:[77..81] with) (NP (NN:[82..85] p16) (NN:[86..97] methylation))) (PP (IN:[98..100] in) (NP (JJ:[101..106] human) (NN:[107..112] colon) (NN:[113..119] cancer))) (.:[119..120] .))) ;section 2 Span:124..158 ;Guan RJ, Fu Y, Holt PR, Pardee AB. (SEC (FRAG (NNP:[124..128] Guan) (NNP:[129..131] RJ) (,:[131..132] ,) (NNP:[133..135] Fu) (NNP:[136..137] Y) (,:[137..138] ,) (NNP:[139..143] Holt) (NNP:[144..146] PR) (,:[146..147] ,) (NNP:[148..154] Pardee) (NN:[155..157] AB) (.:[157..158] .))) ;section 3 Span:162..257 ;Division of Gastroenterology, Brigham & Women's Hospital, Boston, USA. ;rguan@mbcrr.harvard.edu (SEC (FRAG (NNP:[162..170] Division) (IN:[171..173] of) (NNP:[174..190] Gastroenterology) (,:[190..191] ,) (NNP:[192..199] Brigham) (CC:[200..201] &) (NNP:[202..207] Women) (POS:[207..209] 's) (NNP:[210..218] Hospital) (,:[218..219] ,) (NNP:[220..226] Boston) (,:[226..227] ,) (NNP:[228..231] USA) (.:[231..232] .) ('':[234..245] rguan@mbcrr) (VBD:[245..253] .harvard) (.:[253..257] .edu))) ;sentence 4 Span:261..279 ;BACKGROUND & AIMS: (SENT (NP (NN:[261..271] BACKGROUND) (CC:[272..273] &) (NNS:[274..278] AIMS) (::[278..279] :))) ;sentence 5 Span:280..338 ;K-ras mutations are early genetic changes in colon cancer. ;[280..285]:gene-rna:"K-ras" ;[325..337]:malignancy-type:"colon cancer" (SENT (S (NP-SBJ (NN:[280..285] K-ras) (NNS:[286..295] mutations)) (VP (VBP:[296..299] are) (NP-PRD (NP (JJ:[300..305] early) (JJ:[306..313] genetic) (NNS:[314..321] changes)) (PP (IN:[322..324] in) (NP (NN:[325..330] colon) (NN:[331..337] cancer))))) (.:[337..338] .))) ;sentence 6 Span:340..437 ;p16, a tumor-suppressor gene, is inactivated in neoplasms by mutation, ;deletion, or methylation. ;[340..343]:gene-rna:"p16" ;[411..419]:variation-type:"deletion" (SENT (S (NP-SBJ-1 (NP (NN:[340..343] p16)) (,:[343..344] ,) (NP (DT:[345..346] a) (NML (NN:[347..352] tumor) (HYPH:[352..353] -) (NN:[353..363] suppressor)) (NN:[364..368] gene))) (,:[368..369] ,) (VP (VBZ:[370..372] is) (VP (VBN:[373..384] inactivated) (NP-1 (-NONE-:[384..384] *)) (PP (IN:[385..387] in) (NP (NNS:[388..397] neoplasms))) (PP (IN:[398..400] by) (NP-LGS (NN:[401..409] mutation) (,:[409..410] ,) (NN:[411..419] deletion) (,:[419..420] ,) (CC:[422..424] or) (NN:[425..436] methylation))))) (.:[436..437] .))) ;sentence 7 Span:438..575 ;The aims of this study were to determine p16 methylation status and its ;possible association with K-ras mutations in human colon cancer. ;[479..482]:gene-rna:"p16" ;[537..542]:gene-rna:"K-ras" ;[562..574]:malignancy-type:"colon cancer" (SENT (S (NP-SBJ (NP (DT:[438..441] The) (NNS:[442..446] aims)) (PP (IN:[447..449] of) (NP (DT:[450..454] this) (NN:[455..460] study)))) (VP (VBD:[461..465] were) (S-PRP-PRD (NP-SBJ (-NONE-:[465..465] *)) (VP (TO:[466..468] to) (VP (VB:[469..478] determine) (NP (NP (NN:[479..482] p16) (NN:[483..494] methylation) (NN:[495..501] status)) (CC:[503..506] and) (NP (NP (PRP$:[507..510] its) (JJ:[511..519] possible) (NN:[520..531] association)) (PP (IN:[532..536] with) (NP (NP (NN:[537..542] K-ras) (NNS:[543..552] mutations)) (PP (IN:[553..555] in) (NP (JJ:[556..561] human) (NN:[562..567] colon) (NN:[568..574] cancer))))))))))) (.:[574..575] .))) ;sentence 8 Span:577..585 ;METHODS: (SENT (NP (NNS:[577..584] METHODS) (::[584..585] :))) ;sentence 9 Span:586..693 ;DNA isolated from 8 colon cancer cell lines and 41 microdissected human ;colon tissue samples was analyzed. ;[606..618]:malignancy-type:"colon cancer" (SENT (S (NP-SBJ-1 (NP (NN:[586..589] DNA)) (VP (VBN:[590..598] isolated) (NP (-NONE-:[598..598] *)) (PP (IN:[599..603] from) (NP (NP (CD:[604..605] 8) (NML (NN:[606..611] colon) (NN:[612..618] cancer)) (NN:[619..623] cell) (NNS:[624..629] lines)) (CC:[630..633] and) (NP (CD:[634..636] 41) (VBN:[637..651] microdissected) (NML (JJ:[652..657] human) (NN:[659..664] colon) (NN:[665..671] tissue)) (NNS:[672..679] samples)))))) (VP (VBD:[680..683] was) (VP (VBN:[684..692] analyzed) (NP-1 (-NONE-:[692..692] *)))) (.:[692..693] .))) ;sentence 10 Span:694..762 ;p16 methylation status was determined using two analytical methods. ;[694..697]:gene-rna:"p16" (SENT (S (NP-SBJ-1 (NN:[694..697] p16) (NN:[698..709] methylation) (NN:[710..716] status)) (VP (VBD:[717..720] was) (VP (VBN:[721..731] determined) (NP-1 (-NONE-:[731..731] *)) (S-MNR (NP-SBJ (-NONE-:[731..731] *)) (VP (VBG:[732..737] using) (NP (CD:[739..742] two) (JJ:[743..753] analytical) (NNS:[754..761] methods)))))) (.:[761..762] .))) ;sentence 11 Span:763..876 ;The level of p16 expression was determined by reverse-transcription ;polymerase chain reaction and Northern blot. ;[776..779]:gene-rna:"p16" ;[832..842]:gene-protein:"polymerase" (SENT (S (NP-SBJ-1 (NP (DT:[763..766] The) (NN:[767..772] level)) (PP (IN:[773..775] of) (NP (NN:[776..779] p16) (NN:[780..790] expression)))) (VP (VBD:[791..794] was) (VP (VBN:[795..805] determined) (NP-1 (-NONE-:[805..805] *)) (PP-MNR (IN:[806..808] by) (NP (NP (NML (NN:[810..817] reverse) (HYPH:[817..818] -) (NN:[818..831] transcription)) (NN:[832..842] polymerase) (NN:[843..848] chain) (NN:[849..857] reaction)) (CC:[858..861] and) (NP (JJ:[862..870] Northern) (NN:[871..875] blot)))))) (.:[875..876] .))) ;sentence 12 Span:877..935 ;K-ras mutations were determined by DNA sequence analysis. ;[877..882]:gene-rna:"K-ras" (SENT (S (NP-SBJ-1 (NN:[877..882] K-ras) (NNS:[884..893] mutations)) (VP (VBD:[894..898] were) (VP (VBN:[899..909] determined) (NP-1 (-NONE-:[909..909] *)) (PP (IN:[910..912] by) (NP (NN:[913..916] DNA) (NN:[917..925] sequence) (NN:[926..934] analysis))))) (.:[934..935] .))) ;sentence 13 Span:936..1001 ;The DNA methyltransferase activity was determined by microassay. ;[944..961]:gene-protein:"methyltransferase" (SENT (S (NP-SBJ-1 (DT:[936..939] The) (NN:[940..943] DNA) (NN:[944..961] methyltransferase) (NN:[963..971] activity)) (VP (VBD:[972..975] was) (VP (VBN:[976..986] determined) (NP-1 (-NONE-:[986..986] *)) (PP-MNR (IN:[987..989] by) (NP (NN:[990..1000] microassay))))) (.:[1000..1001] .))) ;sentence 14 Span:1002..1141 ;Parental and K-ras-transformed IEC-18 cells were used to determine the ;potential association between K-ras mutations and p16 methylation. ;[1015..1020]:gene-rna:"K-ras" ;[1104..1109]:gene-rna:"K-ras" ;[1125..1128]:gene-rna:"p16" (SENT (S (NP-SBJ-2 (NP (JJ:[1002..1010] Parental) (NML-1 (-NONE-:[1010..1010] *P*))) (CC:[1011..1014] and) (NP (ADJP (NN:[1015..1020] K-ras) (HYPH:[1020..1021] -) (VBN:[1021..1032] transformed)) (NML-1 (NN:[1033..1039] IEC-18) (NNS:[1041..1046] cells)))) (VP (VBD:[1047..1051] were) (VP (VBN:[1052..1056] used) (NP-2 (-NONE-:[1056..1056] *)) (S-ADV (NP-SBJ (-NONE-:[1056..1056] *)) (VP (TO:[1057..1059] to) (VP (VB:[1060..1069] determine) (NP (NP (DT:[1070..1073] the) (JJ:[1074..1083] potential) (NN:[1084..1095] association)) (PP (IN:[1096..1103] between) (NP (NP (NN:[1104..1109] K-ras) (NNS:[1110..1119] mutations)) (CC:[1121..1124] and) (NP (NN:[1125..1128] p16) (NN:[1129..1140] methylation)))))))))) (.:[1140..1141] .))) ;sentence 15 Span:1142..1150 ;RESULTS: (SENT (NP (NNS:[1142..1149] RESULTS) (::[1149..1150] :))) ;sentence 16 Span:1151..1321 ;Methylated p16 was found in 100% of colon cancer cell lines, 55% of colon ;cancers, 54% of adenomas, and 25% of transitional mucosa but not in normal ;colonic epithelium. ;[1162..1165]:gene-rna:"p16" ;[1187..1199]:malignancy-type:"colon cancer" ;[1220..1233]:malignancy-type:"colon cancers" ;[1242..1250]:malignancy-type:"adenomas" (SENT (S (NP-SBJ-1 (VBN:[1151..1161] Methylated) (NN:[1162..1165] p16)) (VP (VBD:[1166..1169] was) (VP (VP (VBN:[1170..1175] found) (NP-1 (-NONE-:[1175..1175] *)) (PP=2 (IN:[1176..1178] in) (NP (NP (NP (CD:[1179..1182] 100) (NN:[1182..1183] %)) (PP (IN:[1184..1186] of) (NP (NML (NN:[1187..1192] colon) (NN:[1193..1199] cancer)) (NN:[1201..1205] cell) (NNS:[1206..1211] lines)))) (,:[1211..1212] ,) (NP (NP (CD:[1213..1215] 55) (NN:[1215..1216] %)) (PP (IN:[1217..1219] of) (NP (NN:[1220..1225] colon) (NNS:[1226..1233] cancers)))) (,:[1233..1234] ,) (NP (NP (CD:[1235..1237] 54) (NN:[1237..1238] %)) (PP (IN:[1239..1241] of) (NP (NNS:[1242..1250] adenomas)))) (,:[1250..1251] ,) (CC:[1252..1255] and) (NP (NP (CD:[1256..1258] 25) (NN:[1258..1259] %)) (PP (IN:[1260..1262] of) (NP (JJ:[1263..1275] transitional) (NN:[1277..1283] mucosa))))))) (CC:[1284..1287] but) (VP (RB:[1288..1291] not) (PP=2 (IN:[1292..1294] in) (NP (JJ:[1295..1301] normal) (JJ:[1302..1309] colonic) (NN:[1310..1320] epithelium)))))) (.:[1320..1321] .))) ;sentence 17 Span:1322..1421 ;Forty-five percent of cancers and 38% of adenomas showed both K-ras ;mutations and p16 methylation. ;[1364..1372]:malignancy-type:"adenomas" ;[1385..1390]:gene-rna:"K-ras" ;[1405..1408]:gene-rna:"p16" (SENT (S (NP-SBJ (NP (NP (CD:[1322..1332] Forty-five) (NN:[1333..1340] percent)) (PP (IN:[1341..1343] of) (NP (NNS:[1344..1351] cancers)))) (CC:[1352..1355] and) (NP (NP (CD:[1357..1359] 38) (NN:[1359..1360] %)) (PP (IN:[1361..1363] of) (NP (NNS:[1364..1372] adenomas))))) (VP (VBD:[1373..1379] showed) (NP (CC:[1380..1384] both) (NP (NN:[1385..1390] K-ras) (NNS:[1391..1400] mutations)) (CC:[1401..1404] and) (NP (CD:[1405..1408] p16) (NN:[1409..1420] methylation)))) (.:[1420..1421] .))) ;sentence 18 Span:1422..1506 ;Of 11 cancers and adenomas with K-ras mutation, 10 specimens showed ;methylated p16. ;[1441..1449]:malignancy-type:"adenomas" ;[1455..1460]:gene-rna:"K-ras" ;[1502..1505]:gene-rna:"p16" (SENT (S (PP-TPC-1 (IN:[1422..1424] Of) (NP (NP (CD:[1425..1427] 11) (NNS:[1428..1435] cancers)) (CC:[1437..1440] and) (NP (NP (NNS:[1441..1449] adenomas)) (PP (IN:[1450..1454] with) (NP (NN:[1455..1460] K-ras) (NN:[1461..1469] mutation)))))) (,:[1469..1470] ,) (NP-SBJ (NP (CD:[1471..1473] 10) (NNS:[1474..1483] specimens)) (PP-1 (-NONE-:[1483..1483] *T*))) (VP (VBD:[1484..1490] showed) (NP (VBN:[1491..1501] methylated) (NN:[1502..1505] p16))) (.:[1505..1506] .))) ;sentence 19 Span:1507..1622 ;In contrast, of 13 adenomas and cancers with wild-type K-ras, only 3 ;specimens showed methylated p16 (P = 0.001). ;[1527..1535]:malignancy-type:"adenomas" ;[1563..1568]:gene-rna:"K-ras" (SENT (S (PP (IN:[1507..1509] In) (NP (NN:[1511..1519] contrast))) (,:[1519..1520] ,) (PP-TPC-1 (IN:[1521..1523] of) (NP (NP (CD:[1524..1526] 13) (NNS:[1527..1535] adenomas) (CC:[1536..1539] and) (NNS:[1540..1547] cancers)) (PP (IN:[1548..1552] with) (NP (NML (JJ:[1553..1557] wild) (HYPH:[1557..1558] -) (NN:[1558..1562] type)) (NN:[1563..1568] K-ras))))) (,:[1568..1569] ,) (NP-SBJ (NP (RB:[1570..1574] only) (CD:[1575..1576] 3) (NNS:[1577..1586] specimens)) (PP-1 (-NONE-:[1586..1586] *T*))) (VP (VBD:[1588..1594] showed) (NP (VBN:[1595..1605] methylated) (NN:[1606..1609] p16)) (PRN (-LRB-:[1610..1611] -LRB-) (S (NP-SBJ (NN:[1611..1612] P)) (VP (SYM:[1613..1614] =) (NP (CD:[1615..1620] 0.001)))) (-RRB-:[1620..1621] -RRB-))) (.:[1621..1622] .))) ;sentence 20 Span:1623..1782 ;Stable transformation of IEC-18 cells with K-ras increased the DNA ;methyltransferase activity, methylated the p16 gene, and suppressed the ;expression of p16. ;[1667..1672]:gene-rna:"K-ras" ;[1691..1708]:gene-protein:"methyltransferase" ;[1734..1737]:gene-rna:"p16" ;[1778..1781]:gene-rna:"p16" (SENT (S (NP-SBJ (NP (JJ:[1623..1629] Stable) (NN:[1630..1644] transformation)) (PP (IN:[1645..1647] of) (NP (NP (NN:[1648..1654] IEC-18) (NNS:[1655..1660] cells)) (PP (IN:[1661..1665] with) (NP (NN:[1667..1672] K-ras)))))) (VP (VP (VBD:[1673..1682] increased) (NP (DT:[1683..1686] the) (NN:[1687..1690] DNA) (NN:[1691..1708] methyltransferase) (NN:[1709..1717] activity))) (,:[1717..1718] ,) (VP (VBD:[1719..1729] methylated) (NP (DT:[1730..1733] the) (NN:[1734..1737] p16) (NN:[1738..1742] gene))) (,:[1742..1743] ,) (CC:[1744..1747] and) (VP (VBD:[1749..1759] suppressed) (NP (NP (DT:[1760..1763] the) (NN:[1764..1774] expression)) (PP (IN:[1775..1777] of) (NP (NN:[1778..1781] p16)))))) (.:[1781..1782] .))) ;sentence 21 Span:1783..1986 ;Treatment with a DNA methylation inhibitor (azadeoxycytidine) resulted in ;reexpression of p16 in K-ras-transformed IEC-18 cells, suggesting that the ;expression of p16 was suppressed by DNA methylation. ;[1874..1877]:gene-rna:"p16" ;[1881..1886]:gene-rna:"K-ras" ;[1948..1951]:gene-rna:"p16" (SENT (S (NP-SBJ (NP (NN:[1783..1792] Treatment)) (PP (IN:[1793..1797] with) (NP (DT:[1798..1799] a) (NN:[1800..1803] DNA) (NN:[1804..1815] methylation) (NN:[1816..1825] inhibitor) (PRN (-LRB-:[1827..1828] -LRB-) (NP (NN:[1828..1844] azadeoxycytidine)) (-RRB-:[1844..1845] -RRB-))))) (VP (VBD:[1846..1854] resulted) (PP-CLR (IN:[1855..1857] in) (NP (NP (NN:[1858..1870] reexpression)) (PP (IN:[1871..1873] of) (NP (NN:[1874..1877] p16))))) (PP-LOC (IN:[1878..1880] in) (NP (ADJP (NN:[1881..1886] K-ras) (HYPH:[1886..1887] -) (VBN:[1887..1898] transformed)) (NN:[1899..1905] IEC-18) (NNS:[1907..1912] cells))) (,:[1912..1913] ,) (S-ADV (NP-SBJ (-NONE-:[1913..1913] *)) (VP (VBG:[1914..1924] suggesting) (SBAR (IN:[1925..1929] that) (S (NP-SBJ-1 (NP (DT:[1930..1933] the) (NN:[1934..1944] expression)) (PP (IN:[1945..1947] of) (NP (NN:[1948..1951] p16)))) (VP (VBD:[1952..1955] was) (VP (VBN:[1956..1966] suppressed) (NP-1 (-NONE-:[1966..1966] *)) (PP (IN:[1967..1969] by) (NP-LGS (NN:[1970..1973] DNA) (NN:[1974..1985] methylation)))))))))) (.:[1985..1986] .))) ;sentence 22 Span:1988..2000 ;CONCLUSIONS: (SENT (NP (NNS:[1988..1999] CONCLUSIONS) (::[1999..2000] :))) ;sentence 23 Span:2001..2121 ;p16 methylation occurs frequently in human colonic adenomas and cancers and ;is closely associated with K-ras mutations. ;[2001..2004]:gene-rna:"p16" ;[2044..2060]:malignancy-type:"colonic adenomas" ;[2044..2051]...[2066..2073]:malignancy-type:"colonic"..."cancers" ;[2105..2110]:gene-rna:"K-ras" (SENT (S (NP-SBJ-2 (NN:[2001..2004] p16) (NN:[2005..2016] methylation)) (VP (VP (VBZ:[2017..2023] occurs) (ADVP-TMP (RB:[2024..2034] frequently)) (PP (IN:[2035..2037] in) (NP (NP (ADJP-1 (JJ:[2038..2043] human) (JJ:[2044..2051] colonic)) (NNS:[2052..2060] adenomas)) (CC:[2061..2064] and) (NP (ADJP-1 (-NONE-:[2064..2064] *P*)) (NNS:[2066..2073] cancers))))) (CC:[2074..2077] and) (VP (VBZ:[2078..2080] is) (ADVP (RB:[2081..2088] closely)) (VP (VBN:[2089..2099] associated) (NP-2 (-NONE-:[2099..2099] *)) (PP-CLR (IN:[2100..2104] with) (NP (NN:[2105..2110] K-ras) (NNS:[2111..2120] mutations)))))) (.:[2120..2121] .))) ;section 24 Span:2125..2170 ;PMID: 10220498 [PubMed - indexed for MEDLINE] (SEC (FRAG (NNP:[2125..2129] PMID) (::[2129..2130] :) (CD:[2131..2139] 10220498) (NN:[2140..2141] -LSB-) (NNP:[2141..2147] PubMed) (::[2148..2149] -) (NN:[2150..2157] indexed) (IN:[2158..2161] for) (NNP:[2162..2170] MEDLINE-RSB-)))