主页实验库实验详情

E-GEOD-65858 GSE65858 transcription profiling by array Homo sapiens

Gene expression patterns and TP53 mutations are associated with HPV RNA status, lymph node metastasis, and survival in head and neck cancer

·发布 2015年6月24日 ·更新 2015年6月27日

270

样本数

270

实验数

芯片平台

实验描述

A growing proportion of head and neck squamous cell carcinomas (HNSCC) is associated with the human papilloma virus (HPV), particularly HPV16. We compare tumors with different HPV16 DNA and RNA (E6*I) status from 290 consecutively recruited HNSCC patients by gene expression profiling and targeted sequencing of 50 genes. We confirm that the HPV16 DNA+ RNA+ tumors are molecularly distinct from the HPV-negative (DNA-) HNSCC and have elevated expression of cell cycle genes and rare TP53 mutations (3.6%, 1/28). We show that tumors with non-transcriptionally active HPV16 (DNA+ RNA-) are similar to HPV DNA- tumors regarding gene expression and frequency of TP53 mutations (47%, 8/17 and 43%, 72/167, respectively). Furthermore, we identify four gene expression clusters. They moderately but significantly differ in overall survival. One cluster exhibits high expression of immune response genes (IR) and contains most of the HPV16 DNA+ RNA+ patients. The IR cluster and disruptive TP53 mutations are associated with lymph node metastasis independent of HPV16 status and we validate each of these associations in another large data set. Consistent with earlier studies, disruptive TP53 mutations are prognostically unfavorable. Our findings underscore the importance of measuring the HPV16 RNA (E6*I) and TP53-mutation status for patient stratification and for the first time identify associations of an immune response-related gene expression cluster and TP53 mutations with lymph node metastasis in HNSCC. A total of 300 samples were considered. Quality control procedures were applied to microarray probe-level intensity files. A total of 270 tumor arrays remained after removing low-quality arrays, duplicate arrays, and arrays from non-HNSCC samples. Expression values were log2-transformed and normalized using RSN.

芯片平台

A-GEOD-10558

Illumina HumanHT-12 V4.0 expression beadchip（270 例）

样本属性

age

35.3401779603012, 38.1437371663244, 40.0465434633812, 40.2655715263518, 40.394250513347, 41.6892539356605, 42.6776180698152, 42.7898699520876, 43.1895961670089, 43.2799452429843, 44.3039014373717, 44.3066392881588, 44.4599589322382, 44.6269678302532, 44.7173169062286, 44.7227926078029, 44.8870636550308, 45.3497604380561, 45.7604380561259, 45.7960301163587, 45.9822039698836, 46.1327857631759, 46.5106091718001, 46.5188227241615, 46.9267624914442, 47.1594798083504, 47.6495550992471, 47.9507186858316, 48.1752224503765, 48.2956878850103, 48.2984257357974, 48.3613963039014, 48.5585215605749, 48.8158795345654, 48.8268309377139, 48.8733744010951, 48.8980150581793, 49.0047912388775, 49.2128678986995, 49.2566735112936, 49.9876796714579, 50.1601642710472, 50.2505133470226, 50.2642026009582, 50.2943189596167, 50.4640657084189, 50.4777549623546, 50.6447638603696, 50.6639288158795, 50.7268993839836, 50.8090349075975, 51.0992470910335, 51.192334017796, 51.2826830937714, 51.4250513347023, 51.4579055441478, 51.5373032169747, 51.6112251882272, 51.6495550992471, 51.7973990417522, 51.8850102669405, 52.0520191649555, 52.1286789869952, 52.2847364818617, 52.3258042436687, 52.3340177960301, 52.4052019164955, 52.4271047227926, 52.4298425735797, 52.5694729637235, 52.621492128679, 52.6242299794661, 52.6817248459959, 52.829568788501, 52.9226557152635, 53.2731006160164, 53.6536618754278, 53.6892539356605, 53.6974674880219, 53.7577002053388, 53.8945927446954, 53.9110198494182, 54.009582477755, 54.0451745379877, 54.1327857631759, 54.1601642710472, 54.2669404517454, 54.3162217659138, 54.3956194387406, 55.1238877481177, 55.3264887063655, 55.3483915126626, 55.4469541409993, 55.6440793976728, 55.7070499657769, 55.7590691307324, 55.854893908282, 55.8932238193018, 55.9534565366188, 56.2518822724162, 56.2956878850103, 56.3394934976044, 56.3613963039014, 56.3969883641342, 56.5229295003422, 56.5667351129363, 56.5749486652977, 56.6543463381246, 56.7173169062286, 56.7693360711841, 56.788501026694, 56.7967145790554, 56.8624229979466, 56.8980150581793, 56.9144421629021, 56.9472963723477, 56.9637234770705, 56.9883641341547, 57.0759753593429, 57.1334702258727, 57.1471594798084, 57.4592744695414, 57.678302532512, 57.7604380561259, 57.8370978781656, 57.8425735797399, 57.9082819986311, 58.0177960301164, 58.031485284052, 58.1957563312799, 58.2833675564682, 58.3381245722108, 58.362765229295, 58.6146475017112, 58.6639288158795, 58.6803559206023, 58.7049965776865, 58.7488021902806, 58.9267624914442, 58.9349760438056, 59.0198494182067, 59.0417522245038, 59.0691307323751, 59.1485284052019, 59.170431211499, 59.2306639288159, 59.2772073921971, 59.3593429158111, 59.4004106776181, 59.62765229295, 59.7754962354552, 59.8932238193018, 60.0301163586585, 60.0328542094456, 60.0684462696783, 60.1177275838467, 60.5475701574264, 61.1060917180014, 61.1416837782341, 61.223819301848, 61.347022587269, 61.3497604380561, 61.3990417522245, 61.6454483230664, 61.8535249828884, 61.9767282683094, 62.1409993155373, 62.5188227241615, 62.5653661875428, 62.6721423682409, 62.7597535934292, 63.0746064339493, 63.2005475701574, 63.5099247091034, 63.7262149212868, 63.8521560574949, 64.0766598220397, 64.3148528405202, 64.3915126625599, 64.3969883641342, 64.4161533196441, 64.5092402464066, 64.5338809034908, 65.4182067077344, 65.6454483230664, 66.0506502395619, 66.0835044490075, 66.4531143052704, 66.8884325804244, 66.9322381930185, 67.0636550308008, 67.3292265571526, 67.4496919917865, 67.605749486653, 67.6358658453114, 68.1095140314853, 68.1505817932923, 68.227241615332, 68.3175906913073, 68.3203285420945, 68.331279945243, 68.4435318275154, 68.6899383983573, 68.9363449691992, 69.0376454483231, 69.0951403148528, 69.2511978097194, 69.2950034223135, 69.7248459958932, 69.7577002053388, 69.7987679671458, 69.8617385352498, 69.8754277891855, 69.8973305954825, 69.9958932238193, 70.0506502395619, 70.0862422997947, 70.0971937029432, 70.113620807666, 70.4010951403149, 70.4093086926762, 70.4941820670773, 70.6830937713895, 70.7132101300479, 70.9815195071869, 70.9979466119097, 71.2388774811773, 71.3045859000684, 71.5099247091034, 71.668720054757, 72.1122518822724, 72.5201916495551, 72.6680355920602, 72.7419575633128, 72.9390828199863, 73.0321697467488, 73.3853524982888, 73.9876796714579, 74.0396988364134, 74.3572895277207, 74.4969199178645, 74.6967830253251, 74.8117727583847, 74.943189596167, 75.2060232717317, 75.3839835728953, 75.709787816564, 76.0766598220397, 76.2135523613963, 76.3504449007529, 76.5503080082135, 77.0458590006845, 77.1170431211499, 77.284052019165, 77.409993155373, 77.6919917864476, 77.7987679671458, 78.0643394934976, 78.8090349075975, 79.0718685831622, 80.2710472279261, 81.7659137577002, 82.0889801505818, 83.482546201232, 85.6454483230664, 85.719370294319, 87.0444900752909, 87.4086242299795

akt1_mutation

0, 1, NA

alcohol

1 to 30, 31 to 60, >60, no

apc_mutation

0, 1, NA

atm_mutation

0, 1, NA

cdh1_mutation

0, 1, NA

cdkn2a_mutation

0, 1, NA

consensus_cluster

Atypical IR 1, Basal 4, Classical 2, Mesenchymal 3

csf1r_mutation

0, 1, NA

distant_metastasis

0, 1

egfr_mutation

0, 1, NA

erbb2_mutation

0, 1, NA

erbb4_mutation

0, 1, NA

fbxw7_mutation

0, 1, NA

fgfr2_mutation

0, 1, NA

fgfr3_mutation

0, 1, NA

flt3_mutation

0, 1, NA

gna11_mutation

0, 1, NA

hpv16_dna_rna

DNA+RNA+, DNA+RNA-, DNA-, NA

hpv_dna

HPV16, NA, Negative, Other HPV

hras_mutation

0, 1, NA

GW_001, GW_003, GW_004, GW_005, GW_006, GW_007, GW_008, GW_009, GW_010, GW_011, GW_012, GW_013, GW_014, GW_015, GW_016, GW_017, GW_018, GW_020, GW_021, GW_022, GW_023, GW_025, GW_026, GW_027, GW_028, GW_029, GW_030, GW_031, GW_032, GW_033, GW_034, GW_035, GW_036, GW_037, GW_038, GW_039, GW_040, GW_041, GW_042, GW_043, GW_044, GW_045, GW_046, GW_047, GW_049, GW_051, GW_052, GW_053, GW_054, GW_056, GW_057, GW_058, GW_059, GW_060, GW_061, GW_062, GW_063, GW_064, GW_065, GW_066, GW_067, GW_068, GW_069, GW_070, GW_071, GW_072, GW_073, GW_074, GW_075, GW_076, GW_077, GW_078, GW_079, GW_080, GW_081, GW_082, GW_083, GW_084, GW_085, GW_086, GW_087, GW_088, GW_089, GW_091, GW_092, GW_093, GW_094, GW_095, GW_096, GW_097, GW_101, GW_102, GW_103, GW_104, GW_105, GW_106, GW_107, GW_108, GW_109, GW_110, GW_111, GW_112, GW_113, GW_115, GW_116, GW_117, GW_118, GW_119, GW_120, GW_122, GW_123, GW_124, GW_125, GW_126, GW_127, GW_128, GW_129, GW_130, GW_131, GW_133, GW_134, GW_135, GW_136, GW_137, GW_138, GW_139, GW_140, GW_141, GW_142, GW_143, GW_144, GW_145, GW_146, GW_147, GW_148, GW_149, GW_150, GW_151, GW_152, GW_153, GW_154, GW_155, GW_156, GW_157, GW_158, GW_159, GW_160, GW_163, GW_164, GW_165, GW_166, GW_167, GW_168, GW_169, GW_170, GW_171, GW_172, GW_173, GW_174, GW_175, GW_177, GW_178, GW_179, GW_180, GW_181, GW_182, GW_183, GW_184, GW_185, GW_186, GW_187, GW_188, GW_189, GW_190, GW_191, GW_192, GW_193, GW_196, GW_197, GW_198, GW_199, GW_200, GW_201, GW_202, GW_203, GW_204, GW_205, GW_206, GW_207, GW_209, GW_210, GW_211, GW_212, GW_214, GW_215, GW_216, GW_217, GW_218, GW_219, GW_220, GW_221, GW_222, GW_223, GW_224, GW_225, GW_226, GW_227, GW_228, GW_229, GW_230, GW_231, GW_233, GW_234, GW_235, GW_236, GW_237, GW_238, GW_239, GW_240, GW_241, GW_242, GW_243, GW_244, GW_245, GW_246, GW_247, GW_248, GW_249, GW_250, GW_251, GW_253, GW_255, GW_256, GW_257, GW_258, GW_262, GW_263, GW_265, GW_266, GW_268, GW_269, GW_271, GW_272, GW_275, GW_280, GW_281, GW_282, GW_283, GW_284, GW_285, GW_286, GW_287, GW_288, GW_289, GW_290, GW_292, GW_293, GW_294, GW_295, GW_296, GW_297, GW_298, GW_299, GW_300, GW_301, GW_302, GW_303, GW_305, GW_306, GW_307

idh1_mutation

0, 1, NA

jak3_mutation

0, 1, NA

kit_mutation

0, 1, NA

n_category

0, 1, 2a, 2b, 2c, 3

notch1_mutation

0, 1, NA

nras_mutation

0, 1, NA

organism

Homo sapiens

1002, 1003, 1004, 1009, 1016, 1017, 1022, 1024, 1025, 1038, 1043, 1051, 1052, 1057, 1058, 1059, 1060, 1063, 1064, 1066, 1067, 1073, 1074, 1098, 1099, 11, 1100, 1107, 1115, 1123, 1137, 1147, 1149, 1150, 1162, 1176, 1178, 1179, 118, 1182, 1184, 1185, 1191, 1192, 120, 1210, 1211, 1212, 1214, 1219, 1234, 1245, 1249, 1252, 1254, 1270, 1281, 1289, 1291, 1305, 1329, 1332, 1357, 1365, 139, 1435, 146, 147, 1508, 154, 1597, 161, 1687, 1717, 1724, 177, 1786, 1808, 182, 1822, 1827, 1835, 1837, 1855, 1872, 188, 1904, 1939, 1962, 198, 20, 2001, 2025, 2029, 2033, 2059, 209, 212, 2240, 23, 2310, 2393, 253, 257, 258, 267, 268, 269, 272, 274, 275, 279, 294, 304, 305, 324, 325, 344, 346, 356, 358, 366, 415, 417, 429, 46, 466, 473, 489, 499, 510, 521, 546, 549, 552, 553, 563, 566, 574, 577, 578, 581, 582, 590, 595, 596, 597, 602, 603, 605, 611, 616, 617, 619, 623, 631, 632, 643, 652, 657, 662, 665, 672, 679, 680, 689, 701, 710, 713, 725, 730, 734, 741, 743, 750, 751, 753, 755, 758, 764, 765, 769, 776, 777, 778, 783, 785, 787, 790, 793, 794, 805, 811, 813, 815, 825, 826, 831, 833, 834, 840, 843, 846, 855, 856, 857, 871, 875, 877, 882, 884, 885, 896, 903, 906, 927, 933, 937, 941, 944, 945, 947, 951, 954, 961, 968, 974, 979, 982, 987, 996

os_event

FALSE, TRUE

packyears

0, 1, 10, 10.3, 111, 112.5, 12, 120, 125, 13, 13.5, 14, 15, 16, 160, 17, 18, 2, 20, 20.3, 22.5, 24, 25, 28, 3, 30, 31, 32, 33, 34, 35, 36, 38, 39, 4, 40, 41, 42, 44, 45, 48, 50, 55, 60, 61, 65, 68, 7, 7.5, 70, 75, 76, 8, 80, 9, 90, NA

pfs

1002, 1003, 1004, 1008, 1009, 1016, 1017, 1022, 1024, 1025, 1035, 1038, 1042, 1043, 1051, 1058, 1060, 1064, 1066, 1067, 1073, 11, 1100, 1107, 1123, 1137, 1147, 115, 1162, 1178, 1179, 118, 1184, 1185, 1191, 1192, 120, 1211, 1212, 1219, 1234, 124, 1245, 1249, 1252, 1254, 1270, 1281, 1289, 1291, 1305, 132, 1329, 1332, 1343, 1357, 136, 1365, 142, 143, 1435, 146, 147, 1508, 154, 157, 158, 159, 161, 162, 166, 1711, 1717, 177, 1771, 1786, 1808, 1822, 1827, 1837, 1855, 188, 189, 1904, 193, 1939, 196, 20, 2001, 2025, 2059, 209, 221, 2240, 228, 23, 2310, 239, 2393, 249, 253, 257, 258, 267, 269, 271, 272, 275, 279, 283, 285, 287, 289, 304, 309, 311, 322, 324, 325, 330, 346, 351, 353, 354, 356, 364, 366, 394, 404, 405, 426, 428, 429, 434, 443, 457, 46, 463, 468, 472, 476, 484, 489, 499, 503, 507, 510, 517, 531, 539, 549, 552, 553, 561, 563, 566, 568, 569, 574, 577, 578, 581, 582, 590, 596, 597, 601, 602, 603, 605, 609, 611, 616, 619, 622, 623, 632, 643, 652, 653, 657, 662, 665, 67, 674, 680, 700, 701, 710, 713, 725, 730, 733, 743, 750, 751, 755, 758, 760, 764, 765, 769, 776, 777, 778, 785, 787, 793, 794, 811, 815, 825, 826, 834, 840, 843, 846, 855, 857, 864, 871, 875, 882, 884, 885, 906, 92, 933, 937, 941, 945, 947, 954, 968, 974, 979, 982, 987, 996

pfs_event

FALSE, TRUE

pik3ca_mutation

0, 1, NA

pten_mutation

0, 1, NA

rb1_mutation

0, 1, NA

ret_mutation

0, 1, NA

sex

female, male

smad4_mutation

0, 1, NA

smo_mutation

0, 1, NA

smoking

No, Yes

src_mutation

0, 1, NA

stk11_mutation

0, 1, NA

t_category

1, 2, 3, 4a, 4b

tp53_mutation

Disruptive, NA, Non-disruptive, WT

tumor_site

cavum oris, hypopharynx, larynx, NA, oropharynx

tumor_type

Primary, relapse, Secondary

uicc_stage

I, II, III, IVA, IVB, IVC

vhl_mutation

0, 1, NA

实验信息

登记号

E-GEOD-65858

GEO 编号

GSE65858

实验类型

transcription profiling by array

物种

Homo sapiens

发布日期

2015年6月24日

更新日期

2015年6月27日

提交者

Maciej Rosolowski、 Gunnar Wichmann

外部链接

ArrayExpress 原始页 NCBI GEO：GSE65858

分析服务

Gene expression patterns and TP53 mutations are associated with HPV RNA status, lymph node metastasis, and survival in head and neck cancer

联系地址

微信公众号