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Series GSE18370 Query DataSets for GSE18370
Status Public on Mar 09, 2010
Title 21T series cell lines show distinct stage-specific gene expression alterations
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Pathologic and epidemiologic evidence has led to a histologic model of breast cancer progression that involves advancement through specific morphologic stages including atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive mammary carcinoma (IMC), although not necessarily always in a linear fashion. Numerous observational studies have examined genetic, epigenetic and gene expression differences in breast tissues representing these different stages of progression, but model systems which would allow for experimental testing of specific factors influencing transition through these stages are scarce. The 21T series cell lines, all originally derived from the same patient with metastatic breast cancer, have been proposed to represent a mammary tumor progression series. We report here that three of the 21T cell lines indeed mimic specific stages of human breast cancer progression (21PT-derived cells, ADH; 21NT-derived cells, DCIS; 21MT-1 cells, IMC) when grown in the mammary fat pad of nude mice, albeit after up to a year post-injection. In order to develop a more rapid, readily manipulatable in vitro assay for examining the biologic differences between these cell lines, we have made use of a 3D Matrigel system. When grown in 3D Matrigel, we have found characteristic morphologies of the three cell lines in which quantifiable aspects of the stage-specific in vivo behaviors (i.e. differences in acinar structure formation, cell polarization, cell cohesiveness, cell proliferation, cell invasion) are re-capitulated in a reproducible fashion. Gene expression profiling has revealed a characteristic pattern for each of the three cell lines. Interestingly, WNT pathway alterations are particularly predominant in the early transition from 21PTci (ADH) to 21NTci (DCIS), whereas alterations in expression of genes associated with control of cell motility and invasiveness phenomena are more prominent in the later transition of 21NTci (DCIS) to 21MT-1 (IMC). This system thus reveals potential therapeutic targets and will provide a means of testing the influences of identified genes on transitions between these stages of pre-malignant to malignant growth.

Keywords: DCIS or IDC vs ADH
 
Overall design RNA derived from three biological replicates of a cell line representing atypical ductal hyperplasia (ADH), Ductal carcinoma in situ (DCIS), and Invasive ductal carcinoma (IDC)
 
Contributor(s) Souter L, Andrews J, Zhang G, Cook A, Postenka C, Al-Katib W, Rodenhiser D, Chambers A, Tuck A
Citation(s) 20458274
Submission date Oct 01, 2009
Last update date Mar 25, 2019
Contact name Ann Chambers
E-mail(s) joseph.andrews@lhsc.on.ca
Phone (519) 685-8430
Organization name London Regional Cancer program
Department Victoria research labs
Street address 790 Commissioner's Road E
City London
State/province Ontario
ZIP/Postal code N6A 4L6
Country Canada
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (9)
GSM458329 PTci bio rep 1
GSM458330 PTci bio rep 2
GSM458331 PTci bio rep 3
Relations
BioProject PRJNA118135

Genespring normalized raw expression level for all probesets, all arrays header descriptions
Systematic
PT1
NT1
MT1
PT2
NT3
NT2
MT3
PT3
MT2
Common
Genbank
Map
Description

Data table
Systematic PT1 NT1 MT1 PT2 NT3 NT2 MT3 PT3 MT2 Common Genbank Map Description
1007_s_at 7821.7 7353.5 446.3 690.7 642.5 707.5 345.5 448.2 289.5 DDR1 U48705 6p21.3
1053_at 1060.7 1209.8 1122.7 1095.3 723.0 1167.4 838.7 440.4 1056.9 RFC2 M87338 7q11.23 "replicative polymerase accessory protein; activator 1; Human replication factor C, 40-kDa subunit (A1) mRNA, complete cds."
117_at 178.7 170.0 23.2 23.8 73.0 38.5 55.1 67.7 84.2 HSPA6 X51757 1q23
121_at 1577.1 1677.4 2187.0 1997.4 2256.6 1798.2 2130.9 2402.1 1752.4 PAX8 X69699 2q12-q14 paired box gene 8
1255_g_at 40.6 63.3 50.4 66.5 43.5 37.5 46.5 57.9 26.6 GUCA1A L36861 6p21.1
1294_at 266.7 284.3 470.3 302.9 409.2 293.4 454.5 402.5 386.0 UBE1L L13852 3p21 ubiquitin-activating enzyme E1-like
1316_at 171.5 111.4 189.6 181.1 184.6 152.1 146.7 166.7 131.9 THRA X55005 17q11.2
1320_at 197.1 151.8 220.9 115.1 118.4 130.0 123.8 151.6 131.6 PTPN21 X79510 14q31.3
1405_i_at 60.6 48.0 456.5 17.1 12.5 32.6 300.1 11.1 644.6 CCL5 M21121 17q11.2-q12 chemokine (C-C motif) ligand 5
1431_at 59.7 43.0 40.3 72.4 85.0 54.1 90.1 91.8 53.2 CYP2E1 J02843 10q24.3-qter
1438_at 859.4 695.5 150.1 38.5 111.9 75.5 166.5 130.3 127.6 EPHB3 X75208 3q21-qter
1487_at 1044.6 911.6 2349.2 2436.6 2998.1 2660.1 3585.3 2698.6 2105.8 ESRRA L38487 11q13
1494_f_at 310.0 252.2 385.2 331.2 347.7 302.3 433.3 431.4 241.2 CYP2A6 M33318 19q13.2
1552256_a_at 1220.0 1724.3 3707.9 3152.7 3266.0 4027.7 7420.2 2998.5 4207.3 SCARB1 NM_005505 12q24.31 "scavenger receptor class B, member 1"
1552257_a_at 2995.5 2802.9 3960.1 2845.2 3297.5 3229.6 3584.7 3777.7 4253.0 KIAA0153 NM_015140 22q13.31 KIAA0153 protein
1552258_at 206.7 245.5 142.1 134.5 136.7 124.3 161.3 148.0 82.9 MGC4677 NM_052871 2p11.2 hypothetical protein MGC4677
1552261_at 233.1 157.4 40.9 18.2 5.1 10.5 27.4 128.0 4.1 WFDC2 NM_080735 20q12-q13.2 WAP four-disulfide core domain 2
1552263_at 211.7 201.5 295.7 696.5 341.4 342.6 273.0 307.8 503.2 MAPK1 NM_138957 22q11.21 mitogen-activated protein kinase 1
1552264_a_at 652.1 602.1 363.5 632.4 586.8 823.9 541.8 669.2 370.0 MAPK1 NM_138957 22q11.21 mitogen-activated protein kinase 1
1552266_at 88.2 20.7 10.0 50.1 13.4 46.9 36.6 62.7 13.1 ADAM32 NM_145004 8p11.22 a disintegrin and metalloproteinase domain 32

Total number of rows: 54675

Table truncated, full table size 6840 Kbytes.




Genespring Normalized NTci/PTci or MT1/PT ci ratios header descriptions
Systematic
aPT Ratio to PT
aPT Average raw
bNT Ratio to PT
bNT Average Raw
cMT-1 Ratio to PT
cMT-1 Average Raw
Common
Genbank
Map
Description

Data table
Systematic aPT Ratio to PT aPT Average raw bNT Ratio to PT bNT Average Raw cMT-1 Ratio to PT cMT-1 Average Raw Common Genbank Map Description
1007_s_at 1.95 2986.87 2.25 2901.19 0.56 360.44 DDR1 U48705 6p21.3
1053_at 0.74 865.45 0.96 1033.42 1.01 1006.10 RFC2 M87338 7q11.23 "replicative polymerase accessory protein; activator 1; Human replication factor C, 40-kDa subunit (A1) mRNA, complete cds."
117_at 0.99 90.05 1.22 93.84 0.79 54.18 HSPA6 X51757 1q23
121_at 0.98 1992.19 0.98 1910.74 1.11 2023.42 PAX8 X69699 2q12-q14 paired box gene 8
1255_g_at 0.95 55.02 0.85 48.09 0.76 41.16 GUCA1A L36861 6p21.1
1294_at 1.06 324.02 1.11 328.95 1.58 436.92 UBE1L L13852 3p21 ubiquitin-activating enzyme E1-like
1316_at 0.99 173.09 0.87 149.37 0.97 156.06 THRA X55005 17q11.2
1320_at 1.01 154.59 0.92 133.39 1.13 158.76 PTPN21 X79510 14q31.3
1405_i_at 1.32 29.60 1.63 31.01 28.59 467.06 CCL5 M21121 17q11.2-q12 chemokine (C-C motif) ligand 5
1431_at 1.02 74.64 0.83 60.71 0.88 61.19 CYP2E1 J02843 10q24.3-qter
1438_at 1.27 342.72 1.46 294.30 1.26 148.06 EPHB3 X75208 3q21-qter
1487_at 0.78 2059.91 0.82 2189.92 1.18 2680.09 ESRRA L38487 11q13
1494_f_at 1.07 357.55 0.93 300.73 1.14 353.21 CYP2A6 M33318 19q13.2
1552256_a_at 0.77 2457.06 1.00 3006.02 1.82 5111.81 SCARB1 NM_005505 12q24.31 "scavenger receptor class B, member 1"
1552257_a_at 1.04 3206.14 1.05 3109.99 1.41 3932.58 KIAA0153 NM_015140 22q13.31 KIAA0153 protein
1552258_at 1.10 163.08 1.15 168.81 0.94 128.77 MGC4677 NM_052871 2p11.2 hypothetical protein MGC4677
1552261_at 0.65 126.44 0.17 57.67 0.15 24.15 WFDC2 NM_080735 20q12-q13.2 WAP four-disulfide core domain 2
1552263_at 1.18 405.34 0.98 295.16 1.25 357.32 MAPK1 NM_138957 22q11.21 mitogen-activated protein kinase 1
1552264_a_at 0.99 651.25 1.04 670.93 0.70 425.08 MAPK1 NM_138957 22q11.21 mitogen-activated protein kinase 1
1552266_at 1.06 67.00 0.39 26.99 0.30 19.90 ADAM32 NM_145004 8p11.22 a disintegrin and metalloproteinase domain 32

Total number of rows: 54675

Table truncated, full table size 6022 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE18370_MT1_vs_NT_1.5_fold_and_greater_changed_P_less_than_0.05.xls.gz 439.1 Kb (ftp)(http) XLS
GSE18370_NT_vs_PT_1.5fold_and_greater_changed_P_less_than_0.05.xls.gz 55.6 Kb (ftp)(http) XLS
GSE18370_RAW.tar 52.0 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data are available on Series record
Processed data provided as supplementary file

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