Functional genomics identifies ABCC3 as a mediator of taxane resistance in HER2-amplified breast cancer.
Breast cancer is a heterogeneous disease with distinct molecular subtypes characterized by differential response to targeted and chemotherapeutic agents. Enhanced understanding of the genetic alterations characteristic of different subtypes is needed to pave the way for more personalized administration of therapeutic agents. We have taken a functional genomics approach using a well-characterized panel of breast cancer cell lines to identify putative biomarkers of resistance to antimitotic agents such as paclitaxel and monomethyl-auristatin-E (MMAE). In vitro studies revealed a striking difference in sensitivity to these agents between cell lines from different subtypes, with basal-like cell lines being significantly more sensitive to both agents than luminal or HER2-amplified cell lines. Genome-wide association studies using copy number data from Affymetrix single nucleotide polymorphism arrays identified amplification of the chromosome 17q21 region as being highly associated with resistance to both paclitaxel and MMAE. An unbiased approach consisting of RNA interference and high content analysis was used to show that amplification and concomitant overexpression of the gene encoding the ABCC3 drug transporter is responsible for conferring in vitro resistance to paclitaxel and MMAE. We also show that amplification of ABCC3 is present in primary breast tumors and that it occurs predominantly in HER2-amplified and luminal tumors, and we report on development of a specific fluorescence in situ hybridization assay that may have utility as a predictive biomarker of taxane resistance in breast cancer.
O'Brien
Carol
C
Department of Oncology, Genentech, Inc, South San Francisco, California 94080, USA.
Cavet
Guy
G
Pandita
Ajay
A
Hu
Xiaolan
X
Haydu
Lauren
L
Mohan
Sankar
S
Toy
Karen
K
Rivers
Celina Sanchez
CS
Modrusan
Zora
Z
Amler
Lukas C
LC
Lackner
Mark R
MR
D000970:Antineoplastic Agents / Q000627:therapeutic use; D054316:Biomarkers, Pharmacological / Q000032:analysis; D001943:Breast Neoplasms / Q000188:drug therapy* / Q000235:genetics; D018270:Carcinoma, Ductal, Breast / Q000188:drug therapy* / Q000235:genetics; D045744:Cell Line, Tumor; D002874:Chromosome Mapping / Q000379:methods; D016000:Cluster Analysis; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D005784:Gene Amplification / Q000502:physiology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D018734:Genes, erbB-2; D023281:Genomics / Q000379:methods; D006801:Humans; D046228:Microarray Analysis; D027425:ATP-Binding Cassette, Sub-Family C Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000502:physiology*; D017239:Paclitaxel / Q000627:therapeutic use; D034622:RNA Interference; D043823:Taxoids / Q000627:therapeutic use*
D000970:Antineoplastic Agents; D054316:Biomarkers, Pharmacological; D027425:ATP-Binding Cassette, Sub-Family C Proteins; D017239:Paclitaxel; D043823:Taxoids; C114462:multidrug resistance-associated protein 3