title: Comparative expression analysis of four breast cancer subtypes versus matched normal tissue from the same patients.
abstract: Gene expression studies have been widely used in an effort to identify signatures that can predict clinical progression of cancer. In this study we focused instead on identifying gene expression differences between breast tumors and adjacent normal tissue, and between different subtypes of tumor classified by clinical marker status. We have collected a set of 20 breast cancer tissues, matched with the adjacent pathologically normal tissue from the same patient. The cancer samples representing each subtype of breast cancer identified by estrogen receptor ER(+/-) and Her2(+/-) status and divided into four subgroups (ER+/Her2+, ER+/Her2-, ER-/Her2+, and ER-/Her2-) were hybridized on Affymetrix HG-133 Plus 2.0 microarrays. By comparing cancer samples with their matched normal controls we have identified 3537 overall differentially expressed genes using data analysis methods from Bioconductor. When we looked at the genes in common of the four subgroups, we found 151 regulated genes, some of them encoding known targets for breast cancer treatment. Unique genes in the four subgroups instead suggested gene regulation dependent on the ER/Her2 markers selection. In conclusion, the results indicate that microarray studies using robust analysis of matched tumor and normal samples from the same patients can be used to identify genes differentially expressed in breast cancer tumor subtypes even when small numbers of samples are considered and can further elucidate molecular features of breast cancer.
authors.affiliation: Serono Research Institute, Systems Biology, 1 Technology Place, Rockland, MA, USA. pmartini@shire.com
authors.forename: Paolo G V
authors.initials: PG
authors.lastname: Martini
authors.forename: Deanne M
authors.initials: DM
authors.lastname: Taylor
authors.forename: Jadwiga
authors.initials: J
authors.lastname: Bienkowska
authors.forename: Jennifer
authors.initials: J
authors.lastname: Jackson
authors.forename: Gregory
authors.initials: G
authors.lastname: McAllister
authors.forename: Heike
authors.initials: H
authors.lastname: Keilhack
authors.forename: Robert K
authors.initials: RK
authors.lastname: Campbell
mesh_terms: D001943:Breast Neoplasms / Q000145:classification / Q000235:genetics* / Q000473:pathology; D049109:Cell Proliferation; D018450:Disease Progression; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006262:Health; D006801:Humans; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics; D011960:Receptors, Estrogen / Q000235:genetics
chemical_list: D018719:Erb-b2 Receptor Tyrosine Kinases; D011960:Receptors, Estrogen