Molecular characterization of irinotecan (SN-38) resistant human breast cancer cell lines

Background

Studies in taxane and/or anthracycline refractory metastatic breast cancer (mBC) patients have shown approximately 30 % response rates to irinotecan. Hence, a significant number of patients will experience irinotecan-induced side effects without obtaining any benefit. The aim of this study was to lay the groundwork for development of predictive biomarkers for irinotecan treatment in BC.

Methods

We established BC cell lines with acquired or de novo resistance to SN-38, by exposing the human BC cell lines MCF-7 and MDA-MB-231 to either stepwise increasing concentrations over 6 months or an initial high dose of SN-38 (the active metabolite of irinotecan), respectively. The resistant cell lines were analyzed for cross-resistance to other anti-cancer drugs, global gene expression, growth rates, TOP1 and TOP2A gene copy numbers and protein expression, and inhibition of the breast cancer resistance protein (ABCG2/BCRP) drug efflux pump.

Results

We found that the resistant cell lines showed 7–100 fold increased resistance to SN-38 but remained sensitive to docetaxel and the non-camptothecin Top1 inhibitor LMP400. The resistant cell lines were characterized by Top1 down-regulation, changed isoelectric points of Top1 and reduced growth rates. The gene and protein expression of ABCG2/BCRP was up-regulated in the resistant sub-lines and functional assays revealed BCRP as a key mediator of SN-38 resistance.

Conclusions

Based on our preclinical results, we suggest analyzing the predictive value of the BCRP in breast cancer patients scheduled for irinotecan treatment. Moreover, LMP400 should be tested in a clinical setting in breast cancer patients with resistance to irinotecan.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-016-2071-1) contains supplementary material, which is available to authorized users.

Unlocking new contrast in a scanning helium microscope

Delicate structures (such as biological samples, organic films for polymer electronics and adsorbate layers) suffer degradation under the energetic probes of traditional microscopies. Furthermore, the charged nature of these probes presents difficulties when imaging with electric or magnetic fields, or for insulating materials where the addition of a conductive coating is not desirable. Scanning helium microscopy is able to image such structures completely non-destructively by taking advantage of a neutral helium beam as a chemically, electrically and magnetically inert probe of the sample surface. Here we present scanning helium micrographs demonstrating image contrast arising from a range of mechanisms including, for the first time, chemical contrast observed from a series of metal–semiconductor interfaces. The ability of scanning helium microscopy to distinguish between materials without the risk of damage makes it ideal for investigating a wide range of systems.

Scanning helium microscopy uses neutral atoms to image traditionally challenging materials (e.g. delicate, insulating and magnetic samples) non-destructively with absolute surface sensitivity. This work reports the first observation of chemical contrast in helium microscopy via inelastic scattering.

Abstract P4-02-02: Targeted molecular characterization of serum derived cell free DNA from metastatic breast cancer patients treated with first-line tamoxifen

Background: Evaluation of cell-free DNA (cfDNA) is a very attractive tool to serve as "liquid biopsy" to define and establish mutational changes in circulating tumor DNA (ctDNA) non-invasively during therapy.

Aim: To identify tumor specific mutations in serum cfDNA associated with resistance against tamoxifen in metastatic breast cancer.

Materials & Methods: Ten metastatic ER-positive breast cancer patients treated with first-line tamoxifen of whom blood sera was available at start therapy, during treatment and at disease progression were selected. DNA was isolated from normal (nDNA) and primary tumor (ptDNA) tissue and from sera (cfDNA). DNA was analyzed with next generation sequencing by the ion-PGM system (Life Technologies) for a panel of 45 cancer genes. This panel included the most frequently mutated genes for breast, colon, prostate and ovarian cancer reported in the Catalogue Of Somatic Mutations In Cancer (Cosmic database, Release 67; cancer.sanger.ac.uk/). In total 1242 exons (∼255kb) were sequenced with 200 to 5000x reads depth coverage. The panel analyzed all exons for 39 genes and only hotspot exons for 6 oncogenes. Variant Caller software (Life Technologies; version 4.16) was applied to detect non-synonymous and stop-gain single nucleotide variants (SNVs) within the sequenced DNA. Hotspot mutations detected in PIK3CA exons 9 and 20 were validated with snapshot multiplex assays.

Results: Variant Caller analyses revealed in total 252 SNVs within the 40 DNAs from tumor tissue and/or serum analyzed which were not detected in normal tissue. Of these, 229 SNVs were novel and not yet reported in the Cosmic database. Mutations were detected for 10 genes in both ptDNA and cfDNA, which enabled us to characterize ctDNA in serum of nine out of ten patients. The discovered mutations were already reported in Cosmic for PIK3CA, TP53, and NF1, but not for CDH1, APC, SMAD4, MLL, AKAP, CREBBP and MLL2. The PIK3CA, TP53 and APC mutations were observed in tumor and sera for 2, 3 and 2 patients, respectively. Mutations in the other genes, except MLL, were unique for individual patients. The mutation for MLL was seen in almost all patients at low frequencies (1-5%). The hotspot mutations in PIK3CA were confirmed with snapshot assays in the sequenced samples and in additional sera. In four patients, Cosmic reported mutations in BRCA1, KAT6B, MAP3K1, MLL2, PTCH1 and PTEN occurred in ctDNA at disease progression while they were not found in the primary tumor nor in preceding sera. The mutation frequencies ranged from 3% for BRCA1 and MAP3K1 to 6% for MLL2. Moreover, mutations for MED12 (3%) and MLL3 (4%), not yet reported in Cosmic, were each observed in two sera at disease progression for two additional patients. The remaining SNVs are currently verified for their authenticity and occurrence in ptDNA and/or ctDNA.

Conclusion: Molecular characterization of tumor and serum derived DNA with targeted next generation sequencing enabled us to identify ctDNA in serum and to detect mutations at disease progression that might play a role in resistance to first-line tamoxifen.

Citation Format: Maurice Jansen, Corine Beaufort, Jean Helmijr, Ronald van Marion, Niels Krol, Kim Monkhorst, Marian van Fessem, Ron van Schaik, Marcel Smid, Marion Meijer van Gelder, Maxime Look, Anita Trapman, Diana Ramirez-Ardila, Irene Lurkin, Ellen Zwarthoff, John Martens, John Foekens, Winand Dinjens, Stefan Sleijfer, Els Berns. Targeted molecular characterization of serum derived cell free DNA from metastatic breast cancer patients treated with first-line tamoxifen [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-02-02.

A highly contrasting scanning helium microscope

We present a scanning helium microscope equipped to make use of the unique contrast mechanisms, surface sensitivity, and zero damage imaging the technique affords. The new design delivers an order of magnitude increase in the available helium signal, yielding a higher contrast and signal-to-noise ratio. These improvements allow the microscope to produce high quality, intuitive images of samples using topological contrast, while setting the stage for investigations into further contrast mechanisms.

Selection of personalized patient therapy through the use of knowledge-based computational models that identify tumor-driving signal transduction pathways

Increasing knowledge about signal transduction pathways as drivers of cancer growth has elicited the development of "targeted drugs," which inhibit aberrant signaling pathways. They require a companion diagnostic test that identifies the tumor-driving pathway; however, currently available tests like estrogen receptor (ER) protein expression for hormonal treatment of breast cancer do not reliably predict therapy response, at least in part because they do not adequately assess functional pathway activity. We describe a novel approach to predict signaling pathway activity based on knowledge-based Bayesian computational models, which interpret quantitative transcriptome data as the functional output of an active signaling pathway, by using expression levels of transcriptional target genes. Following calibration on only a small number of cell lines or cohorts of patient data, they provide a reliable assessment of signaling pathway activity in tumors of different tissue origin. As proof of principle, models for the canonical Wnt and ER pathways are presented, including initial clinical validation on independent datasets from various cancer types.

Imiquimod 5% cream as pretreatment of Mohs micrographic surgery for nodular basal cell carcinoma in the face: a prospective randomized controlled study

BACKGROUND

Imiquimod 5% cream can reduce or clear superficial and small nodular basal cell carcinoma (BCC). It could be used as a pretreatment of Mohs micrographic surgery (MMS) to decrease defect size.

OBJECTIVES

To study if a pretreatment with imiquimod 5% cream decreases defect size after MMS. In addition, to study the effect on the number of Mohs stages and reconstruction time.

METHODS

Seventy patients aged >18 years with a primary nodular BCC in the face were included. The imiquimod group used imiquimod 5% cream for 4 weeks, before MMS. The control group was treated with MMS only. Tumour and defect sizes were measured. We noted the number of Mohs stages, reconstruction time and side-effects.

RESULTS

The median percentage increase in area from tumour size at baseline to the post-MMS defect for the imiquimod group was significantly less compared with the control group, 50% vs. 147% (P < 0·001). A tendency towards fewer Mohs stages in the imiquimod group was observed and the reconstruction time was significantly shorter in this group (P = 0·01).

CONCLUSIONS

Imiquimod 5% cream as pretreatment of MMS significantly reduced the tumour size in primary nodular BCC and reduced the surgical defect size. Further research is necessary to investigate cost-effectiveness.

The landscape of cancer genes and mutational processes in breast cancer

All cancers carry somatic mutations in their genomes. A subset, known as driver mutations, confer clonal selective advantage on cancer cells and are causally implicated in oncogenesis, and the remainder are passenger mutations. The driver mutations and mutational processes operative in breast cancer have not yet been comprehensively explored. Here we examine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of protein-coding genes. The number of somatic mutations varied markedly between individual tumours. We found strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade, and observed multiple mutational signatures, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides. Driver mutations were identified in several new cancer genes including AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3. Among the 100 tumours, we found driver mutations in at least 40 cancer genes and 73 different combinations of mutated cancer genes. The results highlight the substantial genetic diversity underlying this common disease.

Relocatable fixation systems in intracranial stereotactic radiotherapy. Accuracy of serial CT scans and patient acceptance in a randomized design

PURPOSE

The goal was to provide a quantitative evaluation of the accuracy of three different fixation systems for stereotactic radiotherapy and to evaluate patients' acceptance for all fixations.

METHODS

A total of 16 consecutive patients with brain tumours undergoing fractionated stereotactic radiotherapy (SCRT) were enrolled after informed consent (Clinical trials.gov: NCT00181350). Fixation systems evaluated were the BrainLAB® mask, with and without custom made bite-block (fixations S and A) and a homemade neck support with bite-block (fixation B) based on the BrainLAB® frame. The sequence of measurements was evaluated in a randomized manner with a cross-over design and patients' acceptance by a questionnaire.

RESULTS

The mean three-dimensional (3D) displacement and standard deviations were 1.16 ± 0.68 mm for fixation S, 1.92 ± 1.28 and 1.70 ± 0.83 mm for fixations A and B, respectively. There was a significant improvement of the overall alignment (3D vector) when using the standard fixation instead of fixation A or B in the craniocaudal direction (p = 0.037). Rotational deviations were significantly less for the standard fixation S in relation to fixations A (p = 0.005) and B (p = 0.03). EPI imaging with off-line correction further improved reproducibility. Five out of 8 patients preferred the neck support with the bite-block.

CONCLUSION

The mask fixation system in conjunction with a bite-block is the most accurate fixation for SCRT reducing craniocaudal and rotational movements. Patients favoured the more comfortable but less accurate neck support. To optimize the accuracy of SCRT, additional regular portal imaging is warranted.

Abstract P4-02-16: High miRNA26A1 and Low EZH2 Expression Levels Are Associated with Favorable Outcome to Tamoxifen in Advanced Breast Cancer through Similar Molecular Pathways

Background: We showed that decreased expression levels of EZH2 are associated with a favorable outcome to tamoxifen in advanced breast cancer. Furthermore, EZH2 knockdown in MCF7 cells resulted in estrogen receptor (ER) upregulation and increased sensitivity to anti-estrogens. Recently, EZH2 has been identified as a target of miRNA26A1 and miRNA101.

Objective: To associate miRNA26A1 and miRNA101 expression levels with: A) EZH2 and B) molecular pathways and C) outcome to first-line tamoxifen monotherapy for advanced disease.

Materials & Methods: Expression levels of miRNA26A1, miRNA101, EZH2 and references (miRNA-132 and miRNA-374) were measured using quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) in 235 ER-positive primary breast cancer specimens from patients with advanced disease. The levels of expression were related to clinicopathologic factors and disease outcome. Pathway analysis was performed in a subset of 65 ER-positive tumors with available gene expression microarray data available. Computations were performed with STATA and P-values &lt;0.05 were considered statistically significant.

Results: The miRNA26A1 levels were significantly associated with levels of ER, progesterone (PgR), HER2 and EGFR, whereas miRNA101 levels showed significant relations with PgR expression and menopausal status. The miRNA26A1 and miRNA101 levels showed an inverse relation with EZH2 mRNA levels (Spearman Rank Correlation of -0.21 and -0.15, respectively, P&lt;0.05). As continuous variable in univariate analysis, miRNA26A1 (Hazard Ratio (HR) =0.13, 95 % CI: 0.06-0.28) correlated with Time to Progression (TTP), while miRNA101 did not (HR=0.87, 95% CI: 0.70-1.07). In multivariate analysis including traditional predictive factors, the third with highest miRNA26A1 levels (HR=0.49, 95% CI: 0.34-0.72) alone, or combined with the third with lowest EZH2 levels (HR=0.56, 95% CI: 0.35-0.88) were associated with a favorable TTP independently of traditional factors. Pathway analyses identified 2 overlapping, cell cycle, related pathways with two genes (CCNE1and CDC2) differentially expressed (P&lt;0.05) between tumors with high and low levels of miRNA26A1 and EZH2, respectively. Levels of CCNE1 and CDC2 were tested in the 235 tumors and showed as continuous variables also a significant association with TTP (HR=1.27, 95% CI: 1.12-1.45 and HR=1.53, 95% CI: 0.129-1.81).

Conclusions: The miRNA26A1 and miRNA101 levels have an inverse relation with levels of EZH2, however, only miRNA26A1 has predictive value in advanced breast cancer. Pathways comparison between miRNA26A1 and EZH2 identified 2 overlapping cell cycle related pathways and the genes CCNE1 and CDC2. Low levels of EZH2, CCNE1 and CDC2 and high levels of miRNA26A1 are associated with a favorable outcome to tamoxifen therapy.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-02-16.

Complete response of a metastatic gastroesophageal adenocarcinoma on irinotecan-based chemotherapy in a dialysis patient

We present the first case report of a complete response of metastatic gastroesophageal cancer in a chronic hemodialysis patient with irinotecan-based chemotherapy. An elderly dialysis patient presented with diffuse liver metastases by a gastroesophageal adenocarcinoma. He received combination chemotherapy with 5 fluorouracil and irinotecan. After six months of chemotherapy, liver scans show complete remission. The principles, practice, and experience of chemotherapy with irinotecan during dialysis are discussed.