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E-GEOD-10885 GSE10885 transcription profiling by array Homo sapiens

An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors

提交 2008年3月18日 ·发布 2009年4月1日 ·更新 2014年5月1日

488

样本数

244

实验数

芯片平台

相关文献

实验描述

Metaplastic breast cancers (MBC) are aggressive, chemoresistant tumors characterized by lineage plasticity. To advance understanding of their pathogenesis and relatedness to other breast cancer subtypes, 28 MBCs were compared with common breast cancers using comparative genomic hybridization, transcriptional profiling, and reverse-phase protein arrays and by sequencing for common breast cancer mutations. MBCs showed unique DNA copy number aberrations compared with common breast cancers. PIK3CA mutations were detected in 9 of 19 MBCs (47.4%) versus 80 of 232 hormone receptor-positive cancers (34.5%; P = 0.32), 17 of 75 HER-2-positive samples (22.7%; P = 0.04), 20 of 240 basal-like cancers (8.3%; P < 0.0001), and 0 of 14 claudin-low tumors (P = 0.004). Of 7 phosphatidylinositol 3-kinase/AKT pathway phosphorylation sites, 6 were more highly phosphorylated in MBCs than in other breast tumor subtypes. The majority of MBCs displayed mRNA profiles different from those of the most common, including basal-like cancers. By transcriptional profiling, MBCs and the recently identified claudin-low breast cancer subset constitute related receptor-negative subgroups characterized by low expression of GATA3-regulated genes and of genes responsible for cell-cell adhesion with enrichment for markers linked to stem cell function and epithelial-to-mesenchymal transition (EMT). In contrast to other breast cancers, claudin-low tumors and most MBCs showed a significant similarity to a "tumorigenic" signature defined using CD44(+)/CD24(-) breast tumor-initiating stem cell-like cells. MBCs and claudin-low tumors are thus enriched in EMT and stem cell-like features, and may arise from an earlier, more chemoresistant breast epithelial precursor than basal-like or luminal cancers. PIK3CA mutations, EMT, and stem cell-like characteristics likely contribute to the poor outcomes of MBC and suggest novel therapeutic targets. Comparison of reference samples against treatment

参考文献

Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics.

Hennessy BT, Gonzalez-Angulo AM, Stemke-Hale K, Gilcrease MZ, Krishnamurthy S, Lee JS, Fridlyand J, Sahin A, Agarwal R, Joy C, Liu W, Stivers D, Baggerly K, Carey M, Lluch A, Monteagudo C, He X, Weigman V, Fan C, Palazzo J, Hortobagyi GN, Nolden LK, Wang NJ, Valero V, Gray JW, Perou CM, Mills GB

PMID: 19435916

芯片平台

A-GEOD-5325

Agilent UNC Perou Lab Homo sapiens 1X44K Custom Array（12 例）

A-AGIL-14

Agilent Human 1A Microarray 011521 G4110A (2004 annotation)（19 例）

A-GEOD-1390

Agilent Human 1A Oligo UNC custom Microarrays（119 例）

A-AGIL-9

Agilent Human 1A Microarray (V2) 012097 G4110B（94 例）

样本属性

age

--, 24, 25, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 88

BioSourceProvider

Charles Perou - UNC, Mattew Ewend - UNC, Phil Bernard - Utah, Strategene, University of Chicago

dscores unc337

-0.001117469, -0.001378024, -0.00217497, -0.002873519, -0.003405193, -0.003811602, -0.005894239, -0.008820645, -0.011542429, -0.017456137, -0.018129797, -0.018193361, -0.018873674, -0.020824807, -0.021718075, -0.024572099, -0.027772254, -0.030324076, -0.043220129, -0.043433843, -0.046578966, -0.058322786, -0.060366166, -0.070927848, -0.070995094, -0.072230313, -0.074100939, -0.075437208, -0.076956332, -0.077427995, -0.078075617, -0.079277566, -0.085534984, -0.087492828, -0.088074412, -0.089245371, -0.089467593, -0.093314279, -0.100059139, -0.100214475, -0.101088481, -0.103120394, -0.103352612, -0.10398546, -0.106251522, -0.111452396, -0.111825553, -0.113252832, -0.11487527, -0.116155055, -0.121555187, -0.12512537, -0.130368753, -0.131055212, -0.133012108, -0.135281849, -0.136748482, -0.139728878, -0.139970175, -0.141073782, -0.141183574, -0.141196613, -0.141870807, -0.142482868, -0.142681898, -0.148336251, -0.148836373, -0.149187027, -0.152624184, -0.15275454, -0.154199146, -0.15499191, -0.156379224, -0.15699033, -0.15923879, -0.162222572, -0.162483837, -0.163597374, -0.164353074, -0.164728928, -0.165466578, -0.165897449, -0.166806448, -0.167149954, -0.167184068, -0.167243338, -0.168717694, -0.171496071, -0.173309474, -0.17335459, -0.174944045, -0.175019598, -0.177821487, -0.178244007, -0.180655739, -0.182587588, -0.18480251, -0.185911723, -0.187392348, -0.189391589, -0.190093652, -0.19453827, -0.195556923, -0.196194014, -0.199466614, -0.202063014, -0.204552212, -0.209007067, -0.211007856, -0.213057854, -0.219930198, -0.22418812, -0.228123879, -0.231023479, -0.240188822, -0.240369216, -0.246967902, -0.247106233, -0.247608803, -0.256040048, -0.257101319, -0.257652898, -0.273592059, 0.000893689, 0.002466891, 0.002575898, 0.004074075, 0.010829822, 0.01131292, 0.011900463, 0.012214554, 0.012227346, 0.016284962, 0.016442362, 0.01718866, 0.021242022, 0.023299395, 0.026924514, 0.028346589, 0.032427906, 0.035391403, 0.035865658, 0.036467632, 0.03807137, 0.040136558, 0.040847836, 0.041379815, 0.045092888, 0.046289665, 0.04989688, 0.05058388, 0.050682853, 0.051503271, 0.055650828, 0.057844738, 0.05914449, 0.05944229, 0.060468909, 0.06164142, 0.064431265, 0.064809884, 0.068485715, 0.069792578, 0.072543507, 0.074674673, 0.076477925, 0.08086126, 0.083317137, 0.084330757, 0.084596849, 0.085928653, 0.085930885, 0.087448903, 0.087786604, 0.089735024, 0.090605833, 0.091418764, 0.091804097, 0.091992306, 0.096288498, 0.098357355, 0.099093004, 0.10431567, 0.104755066, 0.105908849, 0.106901872, 0.108317434, 0.111592233, 0.112330611, 0.112666502, 0.11318318, 0.113688427, 0.113748459, 0.114004379, 0.116023254, 0.120566521, 0.12062826, 0.123208145, 0.123575485, 0.124895261, 0.125716285, 0.12585664, 0.130689938, 0.133365316, 0.133924899, 0.137394974, 0.138075248, 0.141588937, 0.141702555, 0.142178555, 0.148812671, 0.153505376, 0.153756391, 0.156704858, 0.1567948, 0.157116105, 0.161718724, 0.165300669, 0.168800794, 0.168827946, 0.180559749, 0.182816726, 0.185046936, 0.185552911, 0.186692997, 0.189882962, 0.195473163, 0.198512186, 0.203598567, 0.205320044, 0.208349799, 0.211011596, 0.214928388, 0.215012506, 0.215817398, 0.218022401, 0.218052977, 0.232044838, 0.238798882, 0.241027684, 0.244194942, 0.247607477, 0.296830543

er (1=positive; 0=negative)

--, 0, 1

grade

--, 1, 2, 3

her2 clinical status ihc/fish (1=positive; 0=negative)

--, 0, 1

node status (1=positive=1 or more nodes+; 0=negative)

--, 0, 1, 2

Organism

Homo sapiens

overall survival event (0=alive, 1=dod or doc)

--, 0, 1

overall suvival months

--, 1, 10, 101, 105, 106, 108, 109, 11, 118, 12, 13, 14, 144, 15, 16, 17, 18, 19, 2, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 3, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 4, 41, 42, 43, 44, 46, 47, 48, 5, 51, 53, 54, 55, 56, 57, 6, 60, 62, 64, 65, 68, 7, 70, 72, 74, 76, 8, 81, 83, 9, 94, 96

pam50 predictions plus claudin-low classification (cell line predictor)

Basal, Claudin, Her2, LumA, LumB, Normal

pgr (1=positive; 0=negative)

--, 0, 1

reference

Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

rfs event (0=no relapse, 1=relapsed at any site or died of disease)

--, 0, 1

rfs months

--, 1, 10, 105, 106, 108, 109, 11, 118, 12, 13, 14, 144, 15, 16, 17, 18, 19, 2, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 3, 30, 31, 32, 33, 35, 36, 37, 38, 39, 4, 41, 42, 43, 44, 46, 48, 5, 51, 53, 54, 56, 57, 59, 6, 62, 65, 68, 7, 76, 8, 81, 83, 9, 96

size (1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)

--, 1, 1.5, 2, 3, 4

实验信息

登记号

E-GEOD-10885

GEO 编号

GSE10885

实验类型

transcription profiling by array

物种

Homo sapiens

提交日期

2008年3月18日

发布日期

2009年4月1日

更新日期

2014年5月1日

提交者

Charles M Perou、 Gordon B Mills、 Charles Perou、 Bryan T Hennessy

外部链接

ArrayExpress 原始页 NCBI GEO：GSE10885

分析服务

An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors

联系地址

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