Exon-level microarray analyses identify alternative splicing programs in breast cancer.
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.
Lapuk
Anna
A
Life Sciences Division, Lawrence Berkeley National Laboratory, University of California at Berkeley, Berkeley, California 94720, USA. alapuk@prostatecentre.com
Marr
Henry
H
Jakkula
Lakshmi
L
Pedro
Helder
H
Bhattacharya
Sanchita
S
Purdom
Elizabeth
E
Hu
Zhi
Z
Simpson
Ken
K
Pachter
Lior
L
Durinck
Steffen
S
Wang
Nicholas
N
Parvin
Bahram
B
Fontenay
Gerald
G
Speed
Terence
T
Garbe
James
J
Stampfer
Martha
M
Bayandorian
Hovig
H
Dorton
Shannon
S
Clark
Tyson A
TA
Schweitzer
Anthony
A
Wyrobek
Andrew
A
Feiler
Heidi
H
Spellman
Paul
P
Conboy
John
J
Gray
Joe W
JW
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
D020033:Protein Isoforms; D012333:RNA, Messenger