P3-06-04: Sno/miRNA Expression Via Next Generation Sequencing: Variation in Patients before and after Treatment

Background

Aberrant expression of small RNA molecules has been shown in breast cancer. It is yet unclear if variation exists in small RNA molecule expression in response to treatment. Since next generation sequencing offers more globally sensitive detection of sno and miRNAs, we performed an RNA-seq study to explore patients pre- and post- brief exposure to treatment.

Methods: We sequenced transcriptomes of frozen biopsy samples from 8 breast cancer patients enrolled in a clinical trial for neoadjuvant therapy using trastuzumab (HER2 positive) or bevacizumab (HER2 negative) with chemotherapy. Tumor core biopsies were taken before and after 10 days of either biologic or nab-paclitaxel treatment and stored in OCT compound. Total RNA was extracted and libraries were constructed for the 16 samples using TruSeq (Illumina). We performed 74bp paired-end sequencing with the Illumina GAII platform. Sequences were aligned to the sno/miRNA track (containing 928 miRNAs and 413 snoRNAs) in UCSC and read counts were determined using Bowtie. We performed differential miRNA and snoRNA expression analysis pair-wise in all pre- and post-therapy samples. Given that miRNA deregulation relies on their protein-coding gene targets, we analyzed the predicted targets of the significantly varying miRNAs for functional enrichment.

Results: Each sample had on average 46 million paired-end reads, of which on average 70% were mapped to the human genome. Overall, we detected 138 miRNAs in at least one sample, with each sample expressing 33 miRNAs on average. We detected a total of 11 miRNAs (7%) that showed significant differential expression with treatment. Interestingly, 6 of these miRNAs varied in all patients. The predicted targets of these miRNAs were enriched in DNA-dependent transcription, gene expression, cell proliferation and cell communication. Similarly, we detected 202 snoRNAs in at least one sample, with each sample expressing 87 snoRNAs on average. Of these, we found 21 snoRNAs (10%) to vary significantly upon treatment and 6 of these snoRNAs showed expression changes in all patients.

Conclusions: These results suggest that variation in sno/miRNA expression may play a role in response to treatment. The consistent variation of sno/miRNAs in response to treatment suggests shared small RNA-mediated mechanisms. If validated, these results suggest that next generation sequencing technologies will allow lead to improved methods of stratifying, subclassifying and managing breast cancer.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-06-04.

P1-06-23: Changes in Gene Expression after One Dose of Trastuzumab (T) in HER2+ Breast Cancer Cell Lines Predict Novel Pathways of Response in HER2 Positive Early Stage Breast Cancer

Introduction: Trastuzumab is a targeted therapy against the HER2 cell surface receptor and has greatly improved prognosis for HER2+ breast cancer patients. Despite decades of research, the mechanism of action of T remains unclear and mechanisms of resistance have not been adequately defined. We sought to determine if models of response and resistance in vitro could identify biomarkers in vivo in HER2+ early breast cancer.

Methods: BT474 and UACC812 cell lines were treated with 10ug/ml T for 0 and 24 hours. Fresh tumor core biopsies were taken at a 2 week timepoint after a single dose of T (8mg/m2) from 80 HER2−overexpressing, early breast cancer patients enrolled on a clinical trial of T>T+C. Nucleic acids were extracted using Qiagen AllPrep and were analyzed with Illumina HT12v3 Beadchip arrays. All arrays were processed at the Yale Center for Genome Analysis (West Haven, CT). Clinical response at surgery was defined as pathologic complete response (pCR), objective response (CR+PR=OR) and non-response (SD+PD=NOR) by RECIST criteria. Gene expression was analyzed in Bioconductor using LIMMA analysis. Pathway analysis was performed using the DAVID bioinformatics resource.

Results: We identified gene expression signatures of T response and resistance in HER2+ breast cancer cell lines across 24-hour exposure to trastuzumab. 180-genes changed significantly in a T-sensitive HER2+ cell line (BT474) and 58 genes changed significantly across treatment in a T-resistant HER2+ cell line (UACC812). We applied these signatures to gene expression profiles from early stage HER2+ breast tumors treated with a single dose of T. The BT474 T-responsive signature was enriched among the changes in expression across treatment for responsive patients. The expression change for the BT474 signature genes was also able to partially cluster responsive and resistant breast tumors by outcome. A subset of the UACC812 T-resistance signature was also enriched in the differential between responsive and resistant tumors prior to T treatment.

Pathway analysis based on the direction of change of genes in pCR and sensitive (BT474) cell lines found gland development/differentiation (enrichment score=4.5), DNA synthesis (ES=4.0), chaperone (ES=2.8) and transcriptional machinery (ES=2.2) to be coordinately downregulated in both sensitive cell lines and tumors. This suggests that the downregulation of differentiation pathways seen in our ‘pCR signature’ (Harris etal: AACR 2011) is not an epiphenomenon of cell loss. There were no significant pathways upregulated in both sensitive tumors and cell lines, however discordant genes were enriched in chromatin regulation pathways (ES=4.1). Of note, our previous findings of amplicon gene downregulation in pCR tumors, yet upregulation in cell lines points to a novel mechanism of chromatin modulation heretofor undiscovered in response to T.

Conclusions: These results demonstrate the value of iterative study of in vitro and in vivo response mechanisms in HER2 cell lines and tumors, and the importance of brief exposure studies in understanding the mechanism of response to T, and other targeted therapies.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-06-23.

Surgical and oncologic outcomes in patients with breast cancer undergoing tattooing prior to neoadjuvant chemotherapy

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Background: Neoadjuvant chemotherapy for breast cancer increases the breast preservation rate, but also increases the rate of local recurrence, probably because there is no standard technique to determine the amount of breast tissue to be removed. In 2007 we described a technique where the surgeon maps the extent of a breast tumor, plans a surgical incision, and tattoos the breast prior to the patient receiving neoadjuvant chemotherapy. After the chemotherapy, digital photographs are retrieved that allow the surgeon to precisely reconstruct where the margins of the original tumor were in the breast, and to proceed with a planned operation to remove the entire tumor bed but minimal surrounding breast tissue. The purpose of this study is to describe a series of patients treated with this technique and to evaluate the surgical and oncologic outcomes obtained.

Methods: Data were collected from a prospective breast cancer database and from chart review on all patients treated with this technique at a single institution. Most patients receiving neoadjuvant chemotherapy underwent the tattooing, unless they knew beforehand that they were going to undergo a mastectomy.

Results: Between June 2005 and January 2011, 87 patients underwent breast tattooing followed by chemotherapy. Of patients who have completed subsequent definitive therapy, the initial surgery was mastectomy in 31 and lumpectomy in 53. Most patients’ tumors became nonpalpable following the therapy, and the pathologic complete and partial response rates were 22% and 64% respectively. Of patients who underwent an initial lumpectomy, 5/53 (9%) had positive margins and underwent further surgery (2 mastectomy and 3 wider lumpectomy). With a median follow-up of 36 months, only 1 patient has had an in-breast local recurrence.

Conclusions: These early results clearly show a lower rate of re-excision and a lower rate of local recurrence than commonly reported in the literature for breast preservation following neoadjuvant chemotherapy. The technique warrants wider application and further study.

Evaluation of ER/PR and HER2 status by RNA sequencing in tissue core biopsies from preoperative clinical trial specimens

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Background: Next-generation sequencing for measuring RNA (RNASeq) offer increased sensitivity, dynamic range and provide unbiased detection of all transcripts. To evaluate the clinical utility of such methods, we sequenced entire transcriptomes from fresh-frozen biopsies in a cohort of 120 patients enrolled on a preoperative therapy trial receiving carboplatin, nab paclitaxel and either bevacizumab (HER2-) or trastuzumab (HER2+).

Methods: Total RNA was extracted and amplified from frozen breast core biopsies and libraries constructed using TruSeq (Illumina). Sequencing was performed on the Illumina GAII platform. 75bp reads were mapped using Tophat and transcript abundance in FPKM units (Fragments per kilo-base of mRNA per million reads) calculated using Cufflinks. CLIA approved assays were performed for ER, PR, HER2 (IHC+/- FISH) on patient tumors. Four tumors from each subtype (ER +ve/HER2 -ve; HER2 +ve; ER/HER2 -ve) were analyzed for correlation with clinical status. PAM50 classification will be provided for verification of molecular subtypes.

Results: RNA-Seq library construction/sequencing were successful in 12/12 samples with 50-90% reads mapped. ER +ve tumors ranged in FPKM values from 1.76-22.67 and ER -ve tumors ranged from 0.00-0.79. i.e. ER RNASeq measurements can separate clinical ER status. HER2 +ve tumors ranged in FPKM values from 2.62-21.71 and HER2 -ve tumors from 0.21-1.79. Of note, 7/8 HER2 -ve tumors ranged from 0.21-0.87 with one ‘outlier’ at 1.79±0.3. This outlier was HER2 IHC 2+, FISH ratio 1.1 with 45% of tumor cells with polysomy chromosome 17. Correspondence of ER/PR and HER2 status with molecular subtyping by PAM50 analysis will be presented.

Conclusions: RNASeq has potential to provide in depth analysis of the breast cancer transcriptome and a single analysis test for standard markers. In addition, RNASeq may uncover unexpected expression patterns in conventionally-defined HER2 -ve tumors. If reproducible in larger datasets, this technology may provide both standard and novel information previously unavailable to oncologists and their patients.

Effect of pharmaceutical pre-assessment on post-operative interventions

Focal points

Abstract P6-15-09: Insulin-Like Growth Factor Receptor I (IGF1R) Inhibitors May Be Synergistic with Chemotherapy in Basal Breast Cancer

Background: Preclinical and clinical data show associations between basal breast cancer (BBC) and obesity, insulin resistance and metabolic syndrome suggesting a role for the insulin-like growth factor (IGF) pathway in this disease. We hypothesized that IGF1R targeted therapy will be active in BBC and would enhance the activity of chemotherapeutic agents. We evaluated AG1024, a kinase inhibitor of IGF1R, and Figitumumab, a human anti-IGF1R antibody, in BBC cell lines as monotherapy and in combination with conventional chemotherapeutic agents, doxorubicin or paclitaxel.

Materials and Methods: To evaluate the effect of AG1024, Figitumumab, doxorubicin and paclitaxel, growth assays were conducted using four BBC cell lines (MDA-MB-231, MDA-MB-468, SUM149 and BT20) and the ER positive control cell line, MCF7. Cells were harvested, resuspended in OptiMEM and plated in triplicate at optimal cell densities (50-70% confluent). AG1024 (0-µM), Figitumumab (0-0.585μM), doxorubicin (0-0µM) and paclitaxel (0-20nM) were added after 24-hour incubation. On Day 5, at 70-90% confluence, the cell proliferation Reagent WST-1 (Roche) was added, cells incubated and OD measured as directed by the manufacturer. The percent of surviving cells in each test well was calculated as follows: OD drug-treated well/untreated mean x 100. Each drug combination was assessed in triplicate. Using CalcuSyn (BioSoft), the Median Effects method described by T-C Chou and P. Talaly was used to determine whether or not drug combinations were synergistic or additive. A combination index (CI) <0.90 = synergism, between 0.90 and 1.10 = additive and >1.10 = antagonism. The CI values reported were observed in two or more experiments.

Results: AG1024 produced dose-dependent growth inhibition in all BBC cell lines.

Cytotoxicity of AG1024 (40uM) after a five day incubation.

The hormone-receptor positive MCF7 cell line was the least sensitive to AG1024. Figitumumab had no activity as monotherapy on BBC and control cell lines. Combination therapy with AG1024 and chemotherapy produced synergistic or additive effects in all BBC cell lines. For instance, combining 01µM doxorubicin with 1µM AG1024 produced a synergistic effect in all BBC cell lines except MDA-MB-468.

Combination Indices (CI) of combination therapy experiments.

Similarly, Figitumumab and chemotherapy produced additive or synergistic growth inhibition. Further data on IGF1R levels and phosphotyrosine activity will be presented

Conclusions: AG1024 causes a dose-dependent decrease in cell viability in BBC cell lines produced synergistic cytotoxicity with paclitaxel and doxorubicin. Figitumumab alone failed to have cytotoxic effects on BBC cell lines, however additive or synergistic effects were seen with paclitaxel or doxorubicin in combination with Figitumumab. The combination of IGF1R inhibitors with chemotherapy in BBC should be further explored.

Abstract P3-14-17: Trastuzumab (H) and Rapamycin (R) for Treatment of HER-2 Overexpressing Metastatic Breast Cancer (BC) with Prior Disease Progression on H Based Therapy: Safety and Pharmacodynamic (PD) Results

Background: Preclinical data shows upregulation of the PI3K/AKT pathway and synergistic cytotoxicty between H+R in sensitive and resistant HER-2 overexpressing BC cell lines.

Methods: We designed a phase II clinical trial with an early stopping rule for excess toxicity in the first 4 wks of H+R therapy, defined as ≥3 cases of drug related grade 3 or 4 toxicity observed in the first 9 pts enrolled on trial. We report safety and PD results in 11 pts treated with oral R 6 mg daily + standard dosesand schedule of H. LVEF by ECHO or MUGA was assessed at baseline and every 3 months thereafter; treatment was held for LVEF drop below normal limits or ≥20 percentage points. Pre and post therapy tumor samples were collected when feasible. Circulating tumor (CTC) and endothelial (CEC) cells were collected and analyzed using the Veridex Cell Search System at baseline, wks 1, 2 and 4 and with every restaging.

Results: 11 pts with median age 56 y (range 38-70) treated with H+R were evaluable for safety. Median # cycles was 3 (range 1+ to 12). Non-hematologic grade 3 toxicities in first 4 wks occurred in 3 of the first 9 pts: 1 pt had syncope associated with leucopenia/neutropenia and urinary infection; 1pt had mucositis which responded to dose reduction; 1 pt with known diabetes had grade 3 hyperglycemia, however, this was non-fasting. One pt had grade 3 leucopenia/neutropenia which responded to dose reduction. Grade 3 toxicities for 11 pts in all cycles were as follows: leucopenia/neutropenia (2 pts), non-fasting hyperglycemia (2 pts), syncope (1 pt), hypokalemia (1pt), hyponatremia (1 pt), mucositis (1 pt), rash (2 pts), nail changes (1 pt), thrombosis (1 pt). Infection (urine in 1 pt, skin in 1 pt), anemia (1pt), and elevated PTT (1 pt). One grade 4 non-fasting hyperglycemia occurred in a diabetic pt. LVEF dropped below normal limits and recovered subsequently in 2 pts. Nine pts had baseline and at least one subsequent evaluation for radiographic response by RECIST. Best response was unconfirmed partial response (PR) in 1 pt (8 cycles), stable disease (SD) in 5 pts (12, 6+,6, 3, and 2 cycles) and progression (PD) in 3pts. We combined analysis of AKT pathway markers from 12 baseline and 9 post therapy tissue samples collected on this trial and a phase I study of R +chemotherapy. There were high correlations between baseline AKT pathway markers (mTOR, PTEN, Akt, pAkt, S6K1 and pS6K1; (Spearman's rho-0.401-0.907). This correlation was lost in post therapy samples. Higher mean mTOR levels were seen in non-responders (PD) vs. responders (SD/PR) [p value=0.04]. Eight pts had CTC and CEC results, and were evaluable for response. Baseline CTC levels of >5 cells/7.5 ml were seen in 2/2 pts with PD and 0/6 pts with SD/PR. There was no significant difference in CEC levels between responders and non-responders. Conclusion: R 6 mg daily appears to be well tolerated when combined with standard doses of H. PR in 1 pt and SD for ≥6 months was observed in 2 pts with prior progression on H based therapy. Baseline elevated mTOR level correlates with poor response to R based combinations. Post therapy change in marker expression suggests biologic effect of R.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-14-17.