title: Molecular characterization of breast cancer cell lines by a low-density microarray.
abstract: We designed a low-density microarray carrying 132 DNA capture sequences highly specific for genes known to be differentially expressed among breast tumors and BCC lines or associated with specific tumor properties (cell-cycle alteration, proteolysis, adhesion, hormone sensitivity, etc). We analyzed gene expression in 11 BCC lines among which 6 had already been extensively studied (BT-474, Hs578T, MCF-7, MDA-MB-231, MDA-MB-453, T-47D) and 5 were still poorly characterized (Evsa-T, IBEP-1, IBEP-2, IBEP-3, KPL-1). Some data obtained were verified or extended by real-time polymerase chain reaction (real-time PCR), Northern blotting, Western blotting, immunohistochemistry and cell growth studies. Clustering analysis of the low-density microarray data allowed the sorting of BCC lines into two classes and supported a major discriminatory role for ER alpha, confirming data from previous studies. A few genes that are highly and specifically expressed in one cell line were identified, such as MGB1 (mammaglobin 1) in Evsa-T cells, and PIP (prolactin-inducible protein) in MDA-MB-453 BCC, suggesting an apocrine origin for these latter cells. Two BCC lines (IBEP-1 and IBEP-3) that had been previously characterized as ER alpha-negative, were classified by the low-density microarray among ER alpha-positive lines (MCF-7, T-47D, IBEP-2, BT-474, KPL-1) and were indeed confirmed as receptor-positive (at both mRNA and protein levels) and hormone-responsive cells. In conclusion, our results support the utility of a low-density microarray approach in cases where the cost and exhaustiveness of high-density microarrays may constitute a drawback; for instance, in obtaining a rapid phenotype evaluation in cell populations freshly isolated from breast tumors.
authors.affiliation: Eppendorf Array Technologies, 5000 Namur, Belgium. delongueville.f@eppendorf.be
authors.forename: Francoise
authors.initials: F
authors.lastname: de Longueville
authors.forename: Marc
authors.initials: M
authors.lastname: Lacroix
authors.forename: Anna-Maria
authors.initials: AM
authors.lastname: Barbuto
authors.forename: Vincent
authors.initials: V
authors.lastname: Bertholet
authors.forename: Dominique
authors.initials: D
authors.lastname: Gallo
authors.forename: Denis
authors.initials: D
authors.lastname: Larsimont
authors.forename: Laurence
authors.initials: L
authors.lastname: Marcq
authors.forename: Nathalie
authors.initials: N
authors.lastname: Zammatteo
authors.forename: Sophie
authors.initials: S
authors.lastname: Boffe
authors.forename: Guy
authors.initials: G
authors.lastname: Leclercq
authors.forename: Jose
authors.initials: J
authors.lastname: Remacle
mesh_terms: D019921:Biotinylation; D015152:Blotting, Northern; D015153:Blotting, Western; D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D002448:Cell Adhesion; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000378:metabolism; D047628:Estrogen Receptor alpha / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007091:Image Processing, Computer-Assisted; D007150:Immunohistochemistry; D060785:Mammaglobin A; D009363:Neoplasm Proteins / Q000378:metabolism; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D016133:Polymerase Chain Reaction; D012313:RNA / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013997:Time Factors; D014598:Uteroglobin / Q000378:metabolism
chemical_list: D018076:DNA, Complementary; D047628:Estrogen Receptor alpha; D060785:Mammaglobin A; D009363:Neoplasm Proteins; D012333:RNA, Messenger; C556448:SCGB2A2 protein, human; D012313:RNA; D014598:Uteroglobin