Table 1.
E-cadherin methylation, transcript, protein, and DNA copy number, and six E-cad transcriptional repressor transcript profiles.
| E-cadherin profiles | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mean | Transcript levels | Protein | E-cad transcriptional repressors transcript levels a | ||||||||||
| Cell line b | methylation c | Hu6800d | 9706 cDNA e | U95 f | U133 g | levels h | aCGH i | SNAl1 j,k | SNal2 l,k | TCF3 m,k | TCF8 n,k | TWIST1 o | ZFHX1B p |
| BR:BT-549 | 54 | 4.91 | 0.51 | 4.32 | 4.82 | −1.46 | −0.15 | 5.75 | 7.09 | 6.28 | 7.59 | 6.82 | 3.68 |
| BR:HS578T | 47 | 4.58 | 0.47 | 4.32 | 4.91 | −0.69 | NAp | 5.59 | 10.11 | 5.95 | 8.32 | 6.27 | 4.42 |
| BR:MCF7 | 21 | 9.39 | 2.82 | 9.01 | 8.39 | 1.63 | 0.11 | 5.74 | 4.38 | 6.35 | 3.63 | 3.84 | 3.02 |
| BR:MDA-MB-231 | 13 | 4.32 | 0.21 | 4.32 | 4.87 | −2.62 | −0.37 | 5.41 | 8.16 | 5.91 | 7.42 | 3.49 | 3.32 |
| BR:T47D | 6 | 8.96 | 2.96 | 9.44 | 8.46 | 1.66 | −0.04 | 5.48 | 4.22 | 6.22 | 3.63 | 3.86 | 3.09 |
| CNS:SF-268 | 48 | 4.70 | 0.40 | 4.32 | 4.56 | −2.06 | −0.26 | 5.36 | 6.98 | 5.86 | 7.04 | 6.15 | 5.11 |
| CNS:SF-295 | 43 | 4.32 | 0.66 | 4.32 | 4.99 | −1.37 | 0.33 | 6.33 | 7.32 | 5.89 | 7.18 | 6.30 | 3.37 |
| CNS:SF-539 | 73 | 4.32 | 0.75 | 4.32 | 4.85 | −1.73 | −0.13 | 6.61 | 9.91 | 5.97 | 7.42 | 5.78 | 4.06 |
| CNS:SNB19 | 86 | 5.17 | 0.46 | 4.30 | 4.92 | −1.16 | 0.40 | 5.64 | 6.00 | 6.18 | 6.22 | 6.26 | 3.49 |
| CNS:SNB-75 | 16 | 4.39 | 0.62 | 4.32 | 4.81 | −1.92 | −0.03 | 6.57 | 7.94 | 6.37 | 7.01 | 5.65 | 4.93 |
| CNS:U251 | 93 | 5.29 | 0.39 | 4.30 | 4.83 | −1.74 | −0.10 | 5.51 | 6.39 | 5.98 | 5.61 | 5.43 | 3.84 |
| CO:COLO205 | 8 | 9.52 | 2.34 | 9.50 | 7.77 | 1.08 | −0.14 | 5.97 | 4.26 | 6.11 | 3.81 | 3.74 | 3.09 |
| CO:HCC-2998 | 11 | 7.81 | 1.46 | 8.58 | 6.13 | 1.56 | 0.33 | 5.98 | 4.37 | 6.50 | 3.65 | 4.02 | 2.98 |
| CO:HCT-116 | 9 | 6.29 | 0.60 | 5.90 | 4.97 | −0.16 | 0.03 | 6.19 | 4.44 | 6.42 | 4.52 | 4.16 | 3.12 |
| CO:HCT-15 | 11 | 8.08 | 2.22 | 8.99 | 6.47 | 1.10 | 0.01 | 5.65 | 4.21 | 6.30 | 3.57 | 3.66 | 3.17 |
| CO:HT29 | 8 | 5.75 | 1.53 | 8.50 | 6.05 | 1.51 | −0.01 | 5.72 | 4.36 | 6.26 | 3.70 | 3.64 | 3.19 |
| CO:KM12 | 6 | 7.55 | 1.27 | 8.04 | 6.33 | 0.32 | 0.03 | 5.83 | 4.56 | 6.36 | 4.17 | 3.72 | 3.09 |
| CO:SW-620 |  |
6.75 | 0.80 | 7.02 | 5.20 | 0.07 | 0.12 | 6.17 | 4.97 | 6.18 | 5.18 | 3.61 | 3.12 |
| LC:A549-ATCC | 14 | 6.89 | 0.88 | 6.90 | 5.12 | −0.52 | 0.15 | 5.98 | 4.38 | 6.58 | 5.77 | 3.99 | 3.13 |
| LC:EKVX | 7 | 7.72 | 1.13 | 6.90 | 5.58 | −0.03 | 0.33 | 5.93 | 4.50 | 6.34 | 6.05 | 3.72 | 3.08 |
| LC:HOP-62 | 21 | 4.32 | 0.41 | 4.32 | 4.88 | −1.40 | −0.15 | 6.14 | 5.35 | 6.14 | 6.14 | 5.79 | 3.50 |
| LC:HOP-92 | 7 | 4.32 | 0.30 | 4.32 | 4.71 | −1.76 | 0.21 | 5.89 | 7.75 | 6.57 | 6.95 | 3.99 | 3.12 |
| LC:NCI-H226 | 12 | 6.11 | 0.46 | 4.30 | 4.86 | −1.44 | 0.00 | 5.69 | 7.32 | 6.14 | 6.37 | 5.55 | 3.74 |
| LC:NCI-H23 | 12 | 44.6 | 0.27 | 4.30 | 4.69 | −2.31 | 0.11 | 5.61 | 5.20 | 5.93 | 6.67 | 5.85 | 3.59 |
| LC:NCI-H322M | 9 | 8.08 | 2.36 | 9.25 | 6.63 | 1.80 | NA p | 5.55 | 4.84 | 6.16 | 3.51 | 4.36 | 3.07 |
| LC:NCI-H460 | 41 | 4.32 | 0.58 | 4.30 | 4.90 | −0.55 | 0.46 | 6.09 | 4.95 | 6.50 | 5.66 | 3.64 | 3.42 |
| LC:NCI-H522 | 15 | 4.46 | 0.34 | 4.32 | 4.94 | −1.17 | NA p | 6.07 | 4.32 | 6.24 | 6.74 | 5.09 | 3.17 |
| LE:CCRF-CEM | 88 | 4.75 | 0.39 | 4.32 | 4.99 | −2.58 | 0.22 | 5.62 | 4.39 | 6.39 | 8.17 | 4.08 | 3.19 |
| LE:HL-60 | 85 | 4.46 | 0.35 | 4.32 | 5.24 | −2.59 | 0.44 | 6.07 | 4.29 | 6.50 | 6.12 | 4.37 | 4.43 |
| LE:K-562 | 98 | 5.83 | 0.36 | 4.32 | 4.97 | −3.29 | 0.06 | 6.15 | 4.32 | 6.06 | 4.73 | 3.80 | 5.19 |
| LE:MOLT-4 | 97 | 4.32 | 0.47 | 4.32 | 5.03 | −2.13 | 0.00 | 5.61 | 4.48 | 6.36 | 7.42 | 3.97 | 3.16 |
| LE:RPMI-8226 | 39 | 5.39 | 0.84 | 4.32 | 5.06 | −1.48 | 0.40 | 5.94 | 5.62 | 6.38 | 5.34 | 3.69 | 3.15 |
| LE:SR | 95 | 4.32 | 0.36 | 4.32 | 4.84 | −1.51 | −0.02 | 5.41 | 4.73 | 6.03 | 6.43 | 5.54 | 4.35 |
| ME:LOXIMVI | 85 | 4.32 | 0.52 | 4.32 | 4.79 | −1.64 | −0.17 | 5.66 | 9.98 | 6.11 | 7.54 | 5.06 | 4.00 |
| ME:M14 | 20 | 4.32 | 0.69 | 4.32 | 5.03 | −2.52 | −0.05 | 5.74 | 8.90 | 6.22 | 3.72 | 5.97 | 4.93 |
| ME:MALME-3M | 12 | 7.28 | 1.00 | 9.04 | 6.23 | −0.28 | −0.44 | 5.81 | 8.14 | 6.32 | 3.88 | 4.48 | 4.78 |
| ME:MDA-MB-435 r | 84 | 4.32 | 0.33 | 4.32 | 5.14 | −1.44 | −0.42 | 5.95 | 9.57 | 6.16 | 5.08 | 5.70 | 4.60 |
| ME:MDA-N r | 84 | 4.32 | 0.35 | 4.32 | 4.80 | −1.49 | −0.46 | 5.73 | 9.65 | 5.92 | 5.71 | 6.03 | 5.69 |
| ME:SK-MEL-2 |  |
4.32 | 0.40 | 4.32 | 5.11 | −1.74 | −0.03 | 6.06 | 6.46 | 6.57 | 4.44 | 6.32 | 4.09 |
| ME:SK-MEL-28 | 5.25 | 0.33 | 4.32 | 4.76 | −2.37 | −0.47 | 5.51 | 9.86 | 5.96 | 4.07 | 5.71 | 5.85 | |
| ME:SK-MEL-5 | 80 | 6.89 | 0.58 | 5.13 | 5.23 | −2.13 | −0.23 | 5.81 | 8.90 | 6.43 | 4.36 | 5.64 | 4.31 |
| ME:UACC-257 | 7 | 7.34 | 1.17 | 7.48 | 5.58 | −0.64 | −0.04 | 5.76 | 10.00 | 6.29 | 3.52 | 4.70 | 5.07 |
| ME:UACC-62 | 59 | 4.32 | 0.45 | 4.32 | 4.98 | −3.05 | −0.29 | 6.47 | 8.55 | 6.44 | 5.36 | 5.74 | 4.10 |
| OV:IGROV1 |  |
4.95 | 0.61 | 4.32 | 4.93 | −1.97 | 0.03 | 5.86 | 4.49 | 6.61 | 5.87 | 3.60 | 3.06 |
| OV:OVCAR-3 | 8 | 7.20 | 0.99 | 6.83 | 5.47 | −1.70 | −0.60 | 6.23 | 4.42 | 6.28 | 3.85 | 4.98 | 3.06 |
| OV:OVCAR-4 | 5 | 7.22 | 1.20 | 7.43 | 5.56 | 1.80 | −0.48 | 6.19 | 4.27 | 6.48 | 3.75 | 5.09 | 3.19 |
| OV:OVCAR-5 | 13 | 5.70 | 0.41 | 4.32 | 4.81 | −1.91 | −0.20 | 5.69 | 5.42 | 6.37 | 6.40 | 3.67 | 3.29 |
| OV:OVCAR-8 | 85 | 5.21 | 0.32 | 4.32 | 4.82 | −1.78 | 0.22 | 5.81 | 4.97 | 6.18 | 6.53 | 3.69 | 3.57 |
| OV:OVCAR8/ADR-RES s | 89 | 6.19 | 0.32 | 4.32 | 4.96 | −2.03 | 0.24 | 6.14 | 5.95 | 6.24 | 5.29 | 5.77 | 3.46 |
| OV:SKOV3−3 | 8 | 5.36 | 0.72 | 4.32 | 5.32 | −0.92 | 0.15 | 5.86 | 5.95 | 6.46 | 5.50 | 5.09 | 3.13 |
| PR:DU-145 | 14 | 6.74 | 0.47 | 5.58 | 5.19 | −0.16 | 0.04 | 5.98 | 4.60 | 6.34 | 5.41 | 3.73 | 3.22 |
| PR:PC-3 | 15 | 6.75 | 0.69 | 4.83 | 5.21 | −2.18 | −0.07 | 5.89 | 7.23 | 6.52 | 5.48 | 5.67 | 3.33 |
| RE:786-0 | 87 | 4.58 | 0.44 | 4.32 | 4.69 | −1.87 | 0.10 | 6.25 | 6.57 | 6.18 | 5.97 | 3.58 | 3.40 |
| RE:A498 | 93 | 4.46 | 0.53 | 4.32 | 4.61 | −1.61 | 0.34 | 6.49 | 4.73 | 6.43 | 5.50 | 3.64 | 3.52 |
| RE:ACHN | 10 | 5.81 | 0.58 | 5.51 | 5.01 | −2.16 | 0.35 | 5.61 | 4.73 | 6.20 | 5.76 | 3.56 | 3.70 |
| RE:CAKI-1 | 33 | 6.74 | 0.78 | 4.64 | 4.97 | −2.30 | 0.66 | 6.27 | 4.48 | 6.34 | 5.81 | 5.10 | 3.36 |
| RE:RXF-393 |  |
4.32 | 0.33 | 4.32 | 4.73 | −1.62 | −0.14 | 6.06 | 7.00 | 6.12 | 7.04 | 3.50 | 4.61 |
| RE:SN12C | 74 | 5.55 | 0.29 | 4.32 | 4.96 | −1.25 | 0.72 | 5.76 | 5.42 | 6.43 | 7.03 | 5.58 | 3.39 |
| RE:TK-10 | 99 | 4.32 | 0.27 | 4.32 | 5.02 | −2.25 | −0.03 | 6.25 | 5.41 | 6.52 | 4.68 | 3.83 | 3.30 |
| RE:UO-31 | 12 | 5.78 | 0.43 | 4.32 | 4.07 | −1.73 | 0.29 | 5.86 | 5.16 | 6.19 | 5.95 | 4.68 | 3.46 |
U133 transcript measurement, log2-transformed. Data processed using the RMA algorithm. Gray blocks indicate levels of transcriptional associated with low levels of E-cad expression (see Figure 1).
Tissues of origin are breast (BR), central nervous system (CNS), colon (CO), non-small cell lung cancer (LC). leukemia (LE), melanoma (ME), ovarian (OV), prostate (PR). and renal (RE).
Mean methylation profile of E-cad promoter. The gray and cross hatched blocks are above or within the 20–30% E-cad expression threshold. respectively.
Gene accession number Z35402. Hu6800 oligonucleotide arrays.
Clone ID 416386. cDNA microarrays. Values are ratios from co-hybridization of an individual cell type and a 12-cell line pool.
Fragment name 977_s_at. Affymetrix HG-U95 oligonucleotide microarray, log2-transformed.
Affymetrix fragment identifier 201130_s_at.
Protein levels expressed as log2 of relative protein concentration from reverse phase protein lysate microarrays.
Ploidy-relative DNA content. Values are log2-transformed. Array spot number 1485. BAG number RMC16P004.
Common name Snail, Affymetrix identifier 219480_at. Exemplar Sequence Accession Number NM_005985. Data
Transcriptional repressors chosen as being representative from multiple probe sets.
Common name SLUG. Affymetrix identifier 213139_at, Exemplar Sequence Accession Number AI572079.
Common name E12/E47 gene product, Affymetrix identifier 216647_at, Exemplar Sequence Accession Number AL117663. HG-U133 transcript measurements, log2-transformed.
Common name ZEB1, Affymetrix identifier 212764 at, Exemplar Sequence Accession Number AI806174.
Common name ACS3, Affymetrix identifier 213943_at, Exemplar Sequence Accession Number NM_000474.
Common name ZEB2, Affymetrix identifier 203603_s_at, Exemplar Sequence Accession Number NM_014795
Data not available.
Cell lines considered to be melanomas. See Results section.
Cell line considered to be a doxorubirin-selected, resistant derivative of OVCAR-8. Previously named MCF7/ADR-RES and NCI/ADR-RES. See results section.