Abstract P6-04-12: Pathway Analysis of Primary Human Triple-Negative Breast Cancers

BACKGROUND: Breast cancer is a complex, heterogeneous disease due to vast differences in cellular origin, genetic mutations, metastatic potential, and disease progression. Triple-negative breast cancer (TNBC) is a subtype defined by negative expression of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor-2. Because of its aggressive nature and poor prognosis, TNBC has gained recent attention within the oncology community. Tissue expression profiling with microarrays is a robust and straightforward method to study molecular features of TNBC at a systems level. The goal of this project was to further understand the pathogenesis of TNBC through comprehensive characterization of molecular and pathway signatures, based on analysis of freshly frozen and paraffin-embedded primary tumors from 20 TNBC patients, compared with syngeneic normal breast samples.

METHODS: Microarrary profiling of quadruplet sets of samples (freshly frozen and paraffin-embedded; 80 samples total) was conducted using the Affymetrix Human Gene 1.0 ST array. The differential expression profile of cancer vs. syngeneic normal tissue was calculated for each patient, as well as for combined samples, using the unpaired t-test. Pathway analyses based on gene expression profiling were performed using Pathway Studio (Ariadne Genomics, Inc). Functional enrichment was performed using Fisher's Exact test and Mann-Whitney test.

RESULTS: This analysis demonstrated that TNBC is characterized by a distinct molecular signature which includes genes and pathways of DNA repair, cell cycle, and energy production. Several DNA repair genes were upregulated by at least 2.3-fold, including CHEK1, BLM, NEIL3, PARP1, FANCI, FANCD2 and EXO1 (P <.0001 for each). While several genes in excision-repair pathways (DDB2, RPA1, XAB2 and RAB23A) were downregulated, most genes involved in homologous recombination (BRCA1, BRCA2, RAD54B, RAD51, and RAD51L1), DNA repair synthesis (POLQ and PCNA), and DNA mismatch repair (MLH1, MSH3, PMS1 and PMS2) were upregulated. Analysis of the PARP1 pathway revealed that most upstream and downstream neighbors of PARP1 were significantly upregulated between 2- and 4.5-fold in TNBC. Consistent with previous observations, PARP1 was significantly upregulated by 2.5-fold (P < .0001) in TNBC. Genes involved with cell cycle checkpoint control were also significantly altered, including 4.4-fold, 3.6-fold, and 6.8-fold upregulation of CCNB1, CDC2, and TOP2A, respectively (P < .0001 for each). Of genes involved in metabolic pathways, those involved in purine, folate and pyrimidine metabolism demonstrated changes consistent with active proliferation of TNBC cells. In addition, expression patterns related to inflammation (leukocyte migration, lymphocyte activation, macrophage chemotaxis) and angiogenesis were observed. This finding is consistent with previously described activation of the NFkB pathway and suggestive of an inflammatory component in the pathogenesis of TNBC. CONCLUSIONS : TNBC appears to be characterized by distinct alterations in DNA repair, cell cycle regulation, and metabolism, thus providing a molecular basis for identifying novel therapeutic strategies for this disease.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-04-12.

Efficacy of BSI-201, a poly (ADP-ribose) polymerase-1 (PARP1) inhibitor, in combination with gemcitabine/carboplatin (G/C) in patients with metastatic triple-negative breast cancer (TNBC): Results of a randomized phase II trial

3

Background: TNBC is an aggressive breast cancer subtype that shares molecular and pathologic features with BRCA1-related breast cancers. BRCA-deficient cells are sensitive to inhibition of PARP1, a critical enzyme of cell proliferation and DNA repair, and thus represent a rational target of PARP inhibitor-based cancer therapy. The objectives of this study were to evaluate BSI-201, a potent PARP1 inhibitor, in combination with gemcitabine/carboplatin (G/C) in subjects with metastatic TNBC. Methods: Eligible subjects had measurable disease and had ≤2 prior cytotoxic regimens for ER-, PR-, and HER2-negative metastatic breast cancer. Patients were randomized (1:1) to G/C alone or G/C + BSI-201. Gemcitabine (1000 mg/m2) and carboplatin (AUC=2) were given on days 1 and 8, and BSI-201 (5.6 mg/kg; iv; biweekly) on days 1, 4, 8, and 11 every 21 days. Endpoints were clinical benefit rate (CBR = CR + PR + SD ≥6 months), progression-free survival (PFS) and overall survival (OS). Results: Analyses of the first 86 of a planned 120 patients showed that BSI-201 + G/C had improved CBR, median PFS, and median OS, compared with G/C alone. The frequency and nature of adverse events (AEs) did not differ between arms. Conclusions: This preliminary analysis demonstrates that BSI-201 + G/C significantly improves CBR, PFS, and OS, compared with G/C alone. BSI-201 + G/C was well tolerated, with BSI-201 adding no significant toxicity to G/C. Updated CBR, PFS, and OS for all 120 patients and exploratory correlative analyses of PARP expression and clinical response will be presented.

[Table: see text] [Table: see text]

Efficacy of BSI-201, a poly (ADP-ribose) polymerase-1 (PARP1) inhibitor, in combination with gemcitabine/carboplatin (G/C) in patients with metastatic triple-negative breast cancer (TNBC): Results of a randomized phase II trial

3

The full, final text of this abstract will be available in Part II of the 2009 ASCO Annual Meeting Proceedings, distributed onsite at the Meeting on May 30, 2009, and as a supplement to the June 20, 2009, issue of the Journal of Clinical Oncology.

[Table: see text]

Triple negative breast cancer: a phase 2, multi-center, open-label, randomized trial of gemcitabine/carboplatin (G/C), with or without BSI-201, a PARP inhibitor

Abstract #2120

Background: PARP is a critical enzyme of cell proliferation and DNA repair and BSI-201 has been shown to be a potent inhibitor of PARP-1 in humans. Triple negative breast cancer (TNBC) shares important features with BRCA1-related breast cancer, a validated target for PARP inhibition. Our studies demonstrate that PARP-1 gene expression is statistically significantly upregulated in TNBC compared with normal breast tissue. The primary objective of this study is to assess the Clinical Benefit Rate (CBR=CR+PR+SD > 6 months) of Gemcitabine/Carboplatin with or without BSI-201 in patients with TNBC.
 Methods: Eligible subjects are ≥ 18 years old who had received ≤ 2 prior chemotherapies for metastatic disease with histologically documented breast cancer that is ER-negative, PR-negative, and HER2-negative. Patients were randomized (1:1 ratio) to one of 2 study arms: a) arm 1: G/C alone; b) arm 2: BSI-201 + G/C. G/C was given on days 1 and 8; G = 1000 mg/m2, C at an AUC=2. In study arm 2, BSI-201 was administered I.V. twice weekly (days 1, 4, 8 and 11) at a dose of 5.6 mg/kg. Cycles were defined as being 21 days in duration. Modified RECIST criteria are used to assess tumor response every 6 weeks (every 2 cycles). Subjects who have progressive disease may crossover to receive BSI-201 and continue G/C. Archived tissue samples were retrieved for the assay of cancer related genes including PARP-1 by multiplex quantitative RT-PCR.
 Results: To date, 50 subjects have been enrolled and treated for up to 8 cycles of therapy. Overall 39 of 50 (78%) subjects experienced at least 1 adverse event. The frequency and nature of the AE's do not differ between the two treatment groups. Gene expression profiling results from the first 28 patients enrolled confirm that the cancers of patients enrolled have uniformly low hormone receptor expression, variable HER2 receptor expression and significant upregulation of PARP-1 compared with normal breast tissue.
 Conclusions: This is the first randomized study of a PARP inhibitor in cancer patients. BSI-201 is safe and well tolerated when given in combination with G/C and adverse events observed were consistent with the known safety profiles of G / C regimens. An updated evaluation of toxicity profile and PARP-1 expression analysis will be presented.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2120.

Changes in p53 expression can modify cell shape of ras-transformed fibroblasts and epitheliocytes

p53 plays an important role in restriction of abnormal cell proliferation. Loss of this safeguard function induced by p53 mutations seems to be a key mechanism in oncogenesis. It cannot be excluded however, that in addition to elimination of p53-dependent checkpoints and/or apoptosis p53 mutations may cause additional effects that contribute to oncogenic transformation. In order to analyse the effects of wild-type (wt) and mutant p53 on expression of ras-induced morphological transformation we used the method of computer-assisted morphometry. The following parameters were determined: a) the area covered by the spread cells; b) dispersion and c) elongation of cell contours. The last two indices characterise cell shape. Elongation indicates the degree of bipolarity of cell contour and dispersion-the degree of its multipolarity. Transformation of Rat1 and mouse 10(3) fibroblasts by N-rasasp12 oncogene was accompanied by dramatic decrease of cell area and increase of dispersion and elongation. IAR-2 discoid epitheliocytes expressing exogenous ras oncogene transformed into polarised cells with decreased cell area. Fluorescent microscopic examination of actin cytoskeleton stained with rhodamine-phalloidin had shown that ras-induced transformation of IAR-2 cells is characterised by disappearance of circumferential actin bundle and straight fibers. Neither did we reveal actin stress-fibers in the ras-transformed Rat1 cells. Transduction of p53 cDNAs caused no significant changes in morphometric parameters of non-transformed parental Rat1, IAR-2 and 10(3) cells, but some of the p53 mutants modified cell shape of ras-transformed cells. p53-His273, unlike other tested p53 mutants (Tyr141, His194, Trp248), induced partial reversion of morphological transformation in both Rat1 fibroblasts and IAR-2 epitheliocytes. Its expression led to increase of average cell area, decrease of dispersion and elongation indices, and re-appearance of actin bundles. Exogenous wild-type p53 also caused some reversion of transformed phenotype of Rat/ras cells, but its effect was weaker than that of the p53-His273. In contrast, another p53 mutant p53-His175 was able to enhance ras-induced morphological transformation in p53-deficient murine 10(3) fibroblasts that is consistent with possible involvement of some gain of function activity of mutant p53 in modulation of cell shape. Possible pathways that might be responsible for p53-induced changes of cell morphology are discussed.