title: DNA repair signature is associated with anthracycline response in triple negative breast cancer patients.
abstract: We hypothesized that a subset of sporadic triple negative (TN) breast cancer patients whose tumors have defective DNA repair similar to BRCA1-associated tumors are more likely to exhibit up-regulation of DNA repair-related genes, anthracycline-sensitivity, and taxane-resistance. We derived a defective DNA repair gene expression signature of 334 genes by applying a previously published BRCA1-associated expression pattern to three datasets of sporadic TN breast cancers. We confirmed a subset of 69 of the most differentially expressed genes by quantitative RT-PCR, using a low density custom array (LDA). Next, we tested the association of this DNA repair microarray signature expression with pathologic response in neoadjuvant anthracycline trials of FEC (n = 50) and AC (n = 16), or taxane-based TET chemotherapy (n = 39). Finally, we collected paraffin-fixed, formalin-embedded biopsies from TN patients who had received neoadjuvant AC (n = 28), and tested the utility of the LDA to discriminate response. Correlation between RNA expression measured by the microarrays and 69-gene LDA was ascertained. This defective DNA repair microarray gene expression pattern was significantly associated with anthracycline response and taxane resistance, with the area under the ordinary receiver operating characteristic curve (AUC) of 0.61 (95% CI = 0.45-0.77), and 0.65 (95% CI = 0.46-0.85), respectively. From the FFPE samples, the 69-gene LDA could discriminate AC responders, with AUC of 0.79 (95% CI = 0.59-0.98). In conclusion, a promising defective DNA repair gene expression signature appears to differentiate TN breast cancers that are sensitive to anthracyclines and resistant to taxane-based chemotherapy, and should be tested in clinical trials with other DNA-damaging agents and PARP-1 inhibitors.
authors.affiliation: Dan L Duncan Cancer Center, Baylor College of Medicine, 1 Baylor Plaza BCM 600, Houston, TX 77030, USA.
authors.forename: A A
authors.initials: AA
authors.lastname: Rodriguez
authors.forename: A
authors.initials: A
authors.lastname: Makris
authors.forename: M F
authors.initials: MF
authors.lastname: Wu
authors.forename: M
authors.initials: M
authors.lastname: Rimawi
authors.forename: A
authors.initials: A
authors.lastname: Froehlich
authors.forename: B
authors.initials: B
authors.lastname: Dave
authors.forename: S G
authors.initials: SG
authors.lastname: Hilsenbeck
authors.forename: G C
authors.initials: GC
authors.lastname: Chamness
authors.forename: M T
authors.initials: MT
authors.lastname: Lewis
authors.forename: L E
authors.initials: LE
authors.lastname: Dobrolecki
authors.forename: D
authors.initials: D
authors.lastname: Jain
authors.forename: S
authors.initials: S
authors.lastname: Sahoo
authors.forename: C K
authors.initials: CK
authors.lastname: Osborne
authors.forename: J C
authors.initials: JC
authors.lastname: Chang
mesh_terms: D018943:Anthracyclines / Q000627:therapeutic use*; D000970:Antineoplastic Agents / Q000627:therapeutic use; D000971:Antineoplastic Combined Chemotherapy Protocols / Q000627:therapeutic use; D019540:Area Under Curve; D001943:Breast Neoplasms / Q000188:drug therapy* / Q000235:genetics*; D002986:Clinical Trials as Topic; D003520:Cyclophosphamide / Q000627:therapeutic use; D004260:DNA Repair / Q000235:genetics*; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D015251:Epirubicin / Q000627:therapeutic use; D005260:Female; D005472:Fluorouracil / Q000627:therapeutic use; D020869:Gene Expression Profiling; D006801:Humans; D020360:Neoadjuvant Therapy; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D012372:ROC Curve; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000096:biosynthesis / Q000235:genetics; D011960:Receptors, Estrogen / Q000096:biosynthesis / Q000235:genetics; D011980:Receptors, Progesterone / Q000096:biosynthesis / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D043823:Taxoids / Q000627:therapeutic use
chemical_list: D018943:Anthracyclines; D000970:Antineoplastic Agents; D003520:Cyclophosphamide; D015251:Epirubicin; D005472:Fluorouracil; D018719:Erb-b2 Receptor Tyrosine Kinases; D011960:Receptors, Estrogen; D011980:Receptors, Progesterone; D043823:Taxoids