title: Exon-level microarray analyses identify alternative splicing programs in breast cancer.
abstract: Protein isoforms produced by alternative splicing (AS) of many genes have been implicated in several aspects of cancer genesis and progression. These observations motivated a genome-wide assessment of AS in breast cancer. We accomplished this by measuring exon level expression in 31 breast cancer and nonmalignant immortalized cell lines representing luminal, basal, and claudin-low breast cancer subtypes using Affymetrix Human Junction Arrays. We analyzed these data using a computational pipeline specifically designed to detect AS with a low false-positive rate. This identified 181 splice events representing 156 genes as candidates for AS. Reverse transcription-PCR validation of a subset of predicted AS events confirmed 90%. Approximately half of the AS events were associated with basal, luminal, or claudin-low breast cancer subtypes. Exons involved in claudin-low subtype-specific AS were significantly associated with the presence of evolutionarily conserved binding motifs for the tissue-specific Fox2 splicing factor. Small interfering RNA knockdown of Fox2 confirmed the involvement of this splicing factor in subtype-specific AS. The subtype-specific AS detected in this study likely reflects the splicing pattern in the breast cancer progenitor cells in which the tumor arose and suggests the utility of assays for Fox-mediated AS in cancer subtype definition and early detection. These data also suggest the possibility of reducing the toxicity of protein-targeted breast cancer treatments by targeting protein isoforms that are not present in limiting normal tissues.
authors.affiliation: Life Sciences Division, Lawrence Berkeley National Laboratory, University of California at Berkeley, Berkeley, California 94720, USA. alapuk@prostatecentre.com
authors.forename: Anna
authors.initials: A
authors.lastname: Lapuk
authors.forename: Henry
authors.initials: H
authors.lastname: Marr
authors.forename: Lakshmi
authors.initials: L
authors.lastname: Jakkula
authors.forename: Helder
authors.initials: H
authors.lastname: Pedro
authors.forename: Sanchita
authors.initials: S
authors.lastname: Bhattacharya
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Purdom
authors.forename: Zhi
authors.initials: Z
authors.lastname: Hu
authors.forename: Ken
authors.initials: K
authors.lastname: Simpson
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
authors.forename: Steffen
authors.initials: S
authors.lastname: Durinck
authors.forename: Nicholas
authors.initials: N
authors.lastname: Wang
authors.forename: Bahram
authors.initials: B
authors.lastname: Parvin
authors.forename: Gerald
authors.initials: G
authors.lastname: Fontenay
authors.forename: Terence
authors.initials: T
authors.lastname: Speed
authors.forename: James
authors.initials: J
authors.lastname: Garbe
authors.forename: Martha
authors.initials: M
authors.lastname: Stampfer
authors.forename: Hovig
authors.initials: H
authors.lastname: Bayandorian
authors.forename: Shannon
authors.initials: S
authors.lastname: Dorton
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.forename: Anthony
authors.initials: A
authors.lastname: Schweitzer
authors.forename: Andrew
authors.initials: A
authors.lastname: Wyrobek
authors.forename: Heidi
authors.initials: H
authors.lastname: Feiler
authors.forename: Paul
authors.initials: P
authors.lastname: Spellman
authors.forename: John
authors.initials: J
authors.lastname: Conboy
authors.forename: Joe W
authors.initials: JW
authors.lastname: Gray
mesh_terms: D017398:Alternative Splicing; D001665:Binding Sites; D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D048708:Cell Growth Processes / Q000235:genetics; D045744:Cell Line, Tumor; D005091:Exons; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D046228:Microarray Analysis; D020033:Protein Isoforms; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D014162:Transfection
chemical_list: D020033:Protein Isoforms; D012333:RNA, Messenger