Abstract P5-05-02: Whole Genome In Vivo RNA Interference Screening Identifies the Leukemia Inhibitory Factor Receptor as a Novel Breast Tumor Suppressor

Background: Cancer is caused by mutations in oncogenes and tumor suppressor genes resulting in the deregulation of processes fundamental to the normal behavior of cells. The identification and characterization of oncogenes and tumor suppressors has led to new treatment strategies that have significantly improved cancer outcome. The advent of next generation sequencing has allowed the elucidation of the fine structure of cancer genomes, however, the identification of pathogenic changes is complicated by the inherent genomic instability of cancer cells. Therefore, functional approaches for the identification of novel genes involved in the initiation and development of tumors are critical. Methods: In order to identify functionally important tumor suppressor genes we have conducted the first human whole genome in vivo RNA interference (RNAi) screen. Partially transformed human mammary epithelial cells (HMLEs), which do not form tumors in immunodeficient mice, were infected with the Expression Arrest™ GIPZ lentiviral shRNA library consisting of 62,000 shRNAs targeting the whole human genome, and injected into the mammary fat pad of immunodeficient mice. shRNAs that silenced tumor suppressor genes fully transformed the mammary epithelial cells resulting in tumor formation. Candidate tumor suppressor genes were identified by PCR amplification and sequencing of tumor integrated shRNAs. For validation, candidate tumor suppressor genes were silenced in HMLEs and ectopically expressed in fully transformed breast cancer cells. The effect of modifying gene expression on the transformed phenotype was assessed using soft agar colony formation assays. Clinical significance was determined by comparing expression in normal and cancerous human breast tissue using Oncomine Research. Results and Discussion: Using our novel approach, we identify previously validated tumor suppressor genes including TP53 and MNT, as well as several novel candidate tumor suppressor genes including leukemia inhibitory factor receptor (LIFR). Silencing LIFR expression with multiple shRNA constructs fully transformed human mammary epithelial cells resulting in enhanced colony formation in soft agar (P<0.05). Furthermore, overexpression of LIFR significantly inhibited colony formation in soft agar of fully transformed MDA231 and MCF7 breast cancer cells (P<0.01). In addition, our analysis of clinical data revealed that LIFR expression is significantly decreased in a large percentage of human cancers including breast (P<0.0001), lung (P<0.0001), hepatocellular (P<0.0001) and gastrointestinal tumors (P<0.0001). These results validate LIFR as a previously unidentified highly significant tumor suppressor, and also demonstrate the power of whole genome in vivo RNAi screens as a method for identifying novel genes regulating tumorigenesis.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P5-05-02.

Abstract P4-01-05: Lapatinib Resistance Confers Cross-Resistance to Microtubule Inhibitors in ErbB2-Overexpressing Breast Cancer Cells

ErbB2 gene amplification occurs in approximately 20% of all breast cancers and is associated with an aggressive subtype with poor clinical prognosis. Acquired resistance to erbB2-targeted therapies is a common occurance even in patients who show an initial clinical response to trastuzumab or lapatinib-based regimens. Optimal treatment for relapsed disease following erbB2 targeted therapies has not been defined. Therefore, we sought to evaluate whether cytotoxic agents have cross-resistance to lapatinib in cell lines that have acquired resistance to lapatinib. Here we established a model of acquired lapatinib resistance derived from erbB2 overexpressing breast cancer cell lines, BT474 and SKBR3. Lapatinib resistant cell lines, BTLapR and SKLapR, were generated by growth in the continuous presence of 2.6 uM lapatinib (peak plasma concentration in human subjects) resulting in IC50 of 4.72 uM (BTLapR) and 0.083 uM (BT474) (P<0.0001). IC50 of SKLapR and SKBR3 were 17.72 uM and 0.1637 uM (P<0.0001), respectively. Next, resulting cells were treated with different classes of chemotherapeutics (2 taxanes, 2 vinca-alkaloids, 1 epothilone, 1 anthracycline, 1 antimetabolite, 2 platinums, and 1 alkylating agent) in order to address cross-resistance to lapatinib. BT474 and BTLapR as well as SKBR3 and SKLapR were exposed to each chemotherapeutic agent and cell viability was evaluated at 72h using a cell proliferation assay (AlamarBlue®). We found that BTLapR was significantly cross-resistant to 5 microtubule inhibitors (paclitaxel, docetaxel, vinorelbine, vinblastine, and ixabepilone), but SKLapR was not (shown in table below).

IC 50 of Significant Drugs on Lapatinib Resistant BT474 cells

Previous studies have shown that resistance to lapatinib can switch cell survival signaling from the erbB2 to ER pathway, and that ER signaling can stimulate beta III tubulin expression. We therefore hypothesize the differential responses to microtubule inhibitors in BTLapR and SKLapR might be explained by the fact that BT474 has both estrogen (ER) and progesterone receptor (PR), but SKBR3 express neither. Moreover, beta-III tubulin is known to be a key resistance mechanism of microtubule inhibition. Western blot analysis of baseline protein expression in both acquired lapatinib-resistant and parental cells indicates that ER signaling is involved in stimulating beta III tubulin and is linked to the development of resistance to microtubule inhibitors. These findings point to a potential mechanism to address cross resistance between lapatinib and microtubule-interacting agents, which could have potential clinical implications when considering salvage therapies following lapatinib treatment.

Current status and future potential of somatic mutation testing from circulating free DNA in patients with solid tumours

Genetic alterations can determine the natural history of cancer and its treatment response. With further advances in DNA sequencing technology, multiple novel genetic alterations will be discovered which could be exploited as prognostic, predictive and pharmacodynamic biomarkers in the development and use of cancer therapeutics. As such, the importance in clinical practice of efficient and robust somatic mutation testing in solid tumours cannot be overemphasized in the current era of personalized medicine. However, significant challenges remain regarding the testing of genetic biomarkers in clinical practice. Reliance on archived formalin fixed, paraffin embedded tumour, obtained from diagnostic biopsies, for testing somatic genetic alterations could restrict the scientific community in asking relevant questions about a patient's cancer biology. Problems inherent with using formalin fixed, archival tissue are well recognized and difficult to resolve. It could be argued that to achieve rapid and efficient incorporation of genetic biomarkers into clinical practice, somatic mutation testing in cancer patients should be simpler, less invasive using a readily available clinical sample, whilst maintaining robustness and reproducibility. In this regard, use of circulating free DNA (cfDNA) from plasma or serum as an alternative and/or additional source of DNA to test cancer specific genetic alterations is an attractive proposition. In light of encouraging results from recent studies, this mini review will discuss the current role and future potential of somatic mutation testing from circulating or cell free DNA derived from the blood of patients with solid tumours.

Phase II study of cisplatin and imatinib in advanced salivary adenoid cystic carcinoma

Patients with adenoid cystic carcinoma of the salivary glands show over-expression of KIT in a high proportion of cases. Options for systemic treatment are limited in locally advanced and metastatic disease. We explored the efficacy of imatinib and cisplatin combined in this group of patients. A Gehan's two-stage, phase II trial was conducted on 28 patients. Those with progressive, locally advanced, and metastatic disease with an over-expression of KIT were treated with single agent imatinib 800 mg daily for two months, followed by a combination of imatinib 400mg daily and cisplatin 80 mg/m(2) at four-weekly intervals for six cycles. This was followed by maintenance single agent imatinib 400mg daily until the disease progressed. Response was monitored using fluorodeoxyglucose positron emission tomography (FDG-PET) and morphological imaging using computed tomography, magnetic resonance, and chest radiographs (CT/MRI/CXR). Morphological imaging showed partial response in three of 28 patients, and five patients showed a response on FDG-PET. In addition, 19 patients had useful stabilisation of disease. The median time to progression and overall survival was 15 months (range 1-43) and 35 months (range 1-75), respectively. The combination of imatinib and cisplatin was reasonably well tolerated. This combination may provide stabilisation in locally advanced and metastatic adenoid cystic carcinoma of the salivary glands.

Issues on fit-for-purpose validation of a panel of ELISAs for application as biomarkers in clinical trials of anti-Angiogenic drugs

Background:

Successful introduction of new anticancer agents into the clinic is often hampered by a lack of qualified biomarkers. Studies have been conducted of 17 ELISAs representing a potential panel of pharmacodynamic/predictive biomarkers for drugs targeted to tumour vasculature.

Methods:

The fit-for-purpose approach to method validation was used. Stability studies were performed using recombinant proteins in surrogate matrices, endogenous analytes in healthy volunteer and cancer patient plasma. The impact of platelet depletion was investigated.

Results:

Method validation focused on measuring precision and showed that 15 of the 17 assays were within acceptable limits. Stability at −80°C was shown for 3 months with all recombinant proteins in surrogate matrices, whereas under the same conditions instability was observed with KGF in platelet-rich and platelet-depleted plasma, and with PDGF-BB in platelet-depleted plasma from cancer patients. For measurement of extracellular circulating analytes, platelet depletion should be conducted before freezing of plasma to prevent release of PDGF-BB, FGFb and VEGF-A. A protocol was developed to remove >90% platelets from plasma requiring centrifugation at 2000 g for 25 min.

Conclusions:

These studies highlight the need for assay validation and crucial assessment of sample handling issues before commencement of biomarker analysis in clinical trials.

Considerations for the use of plasma cytokeratin 18 as a biomarker in pancreatic cancer

BACKGROUND

Enzyme-linked immunoassays of full-length (M65) and/or caspase-cleaved (M30) cytokeratin 18 (CK18) released from epithelial cells undergoing necrosis and/or apoptosis, respectively, may have prognostic or predictive biomarker utility in a range of solid tumour types. Characterisation of baseline levels of circulating full length and cleaved CK18 specifically in patients with pancreatic cancer.

METHODS

Plasma samples from 103 patients with pancreatic cancer stored at -80 degrees C were assayed for M65 and M30 levels. The median (inter-quartile range (IQR)) duration of plasma storage was 34 (23-57) months. Patients with metastatic disease (n=19) were found to have greater median (IQR) M65 levels (1145 (739-1698) U l(-1)) compared with the locally advanced (n=20; 748 (406-1150) U l(-1)) and resected (n=64; 612 (331-987) U l(-1)) patients (P=0.002). Elevated M65 levels were associated with poorer overall survival on univariate (P<0.001) but not multivariate (P=0.202) analysis. M65 concentrations also exhibited significant associations with concurrent serum-bilirubin levels (P<0.001) and the duration of plasma storage (P<0.001).

CONCLUSIONS

Baseline plasma CK18 levels in pancreatic cancer are affected by the presence of obstructive jaundice and prolonged plasma storage. Clinical biomarker studies utilising serial CK18 levels are warranted in pancreatic cancer, provided consideration is given to these potentially confounding factors.

Truncated p95erbB2 Isoforms Are Capable of Transforming Human Mammary Epithelial Cells

Background:Objective clinical response to trastuzumab monotherapy in erbB2-amplified first line metastatic breast cancer is 34% (Vogel, et al., JCO 20: 719-26, 2002). Amongst patients who respond, most develop resistance (defined by disease progression on trastuzumab). One proposed mechanism of trastuzumab resistance is proteolytic cleavage of erbB2 receptor from its full-length (p185) form into truncated, constitutively active p95. Increased expression of p95erbB2 correlates with increased nodal involvement and poor clinical outcome. Because p95erbB2 lacks the trastuzumab binding epitope, expression may designate patients who would be suitable for treatment with erbB2 kinase inhibitors.Materials and Methods:Recombinant p185erbB2 and p95erbB2 constructs were stably expressed in several cell types via retroviral vector. Additionally, an intracellular form of p95erbB2 that arises via alternative translation and an intracellular p95erbB2 construct containing two copies of a nuclear localization sequence were also expressed. Expression and proper subcellular localization of constructs were confirmed by cell fractionation, western blot analysis and confocal microscopy. Transformation of human mammary epithelial (HMEC) and NIH3T3 cells by p185erbB2 and p95erbB2 isoforms was evaluated by anchorage independent growth using a quantitative fluorescent soft agar assay, and effects on migration and invasion of these cells were investigated by wound-healing and transwell assays. Cells transfected with oncogenic Ras or empty vector were used as positive and negative controls in these experiments.Results and Discussion:Recombinant p185erbB2 and p95erbB2 constructs were stably expressed in HMEC and NIH3T3 cells, and were correctly directed to the cell membrane; nuclear targeted intracellular p95erbB2 was correctly localized to the cell nucleus. Both p185 erbB2 and membrane-bound truncated p95erbB2 were sufficient to transform HMEC cells as compared to empty vector control transfected cells [mean fluorescence intensity empty vector control 2480 ± 464 (1 standard deviation); mean fluorescence intensity p185erbB2 9208 ± 2528, p= 0.0106; mean fluorescence intensity p95erbB2 6615 ± 1588, p= 0.0124)] as was the positive control oncogenic Ras (mean fluorescence intensity 4350 ± 433, p=0.0069). Interestingly, nuclear-targeted p95erbB2 was also sufficient to transform HMEC cells (mean fluorescence intensity 6492 ± 818, p=0.0018). These data support the hypothesis that truncated p95erbB2 species may be major pathogenic drivers in erbB2-amplified cancers. P95erbB2 therefore represents an attractive target for diagnosis and treatment of erbB2+ breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3136.

A small molecule inhibitor of XIAP induces apoptosis and synergises with vinorelbine and cisplatin in NSCLC

Background:

Evasion of apoptosis contributes to the pathogenesis of solid tumours including non-small cell lung cancer (NSCLC). Malignant cells resist apoptosis through over-expression of inhibitor of apoptosis proteins (IAPs), such as X-linked IAP (XIAP).

Methods:

A phenylurea-based small molecule inhibitor of XIAP, XIAP antagonist compound (XAC) 1396-11, was investigated preclincally to determine its ability to sensitise to clinically relevant cytotoxics, potentially allowing dose reduction while maintaining therapeutic efficacy.

Results:

XIAP protein expression was detected in six NSCLC cell lines examined. The cytotoxicity of XAC 1396-11 against cultured NSCLC cell lines in vitro was concentration- and time-dependent in both short-term and clonogenic assays. XAC 1396-11-induced apoptosis was confirmed by PARP cleavage and characteristic nuclear morphology. XAC 1396-11 synergised with vinorelbine±cisplatin in H460 and A549 NSCLC cells. The mechanism of synergy was enhanced apoptosis, shown by increased cleavage of caspase-3 and PARP and by the reversal of synergy by a pan-caspase inhibitor. Synergy between XAC 1396-11 and vinorelbine was augmented by optimising drug scheduling with superior effects when XAC 1396-11 was administered before vinorelbine.

Conclusion:

These preclinical data suggest that XIAP inhibition in combination with vinorelbine holds potential as a therapeutic strategy in NSCLC.

Results of a residential indoor PM2.5 sampling program before and after a woodstove changeout

During 2005-2007, a woodstove changeout program was conducted in a Rocky Mountain valley community in an effort to reduce ambient levels of PM(2.5). In addition to changes in ambient PM(2.5), an opportunity was provided to evaluate the changes in indoor air quality when old stoves were replaced with US Environmental Protection Agency (EPA)-certified woodstoves. PM(2.5) samples were measured in 16 homes prior to and following the changeout. For each sampling event, PM(2.5) mass was continuously measured throughout the 24-h sampling periods, and organic/elemental carbon (OC/EC) and associated chemical markers of woodsmoke were measured from quartz filters. Results showed that average PM(2.5) concentrations and maximum PM(2.5) concentrations were reduced by 71% and 76%, respectively (as measured by TSI DustTraks). Levoglucosan was reduced by 45% following the introduction of the new woodstove. However, the concentrations of resin acids, natural chemicals found in the bark of wood, were increased following the introduction of the new woodstove. There were no discernible trends in methoxphenol levels, likely due to the semi-volatile nature of the species that were measured. Although there is some uncertainty in this study regarding the amount of ambient PM infiltration to the indoor environment, these findings demonstrated a large impact on indoor air quality following this intervention.

PRACTICAL IMPLICATIONS

Emissions from residential woodstoves are an important air quality issue (both indoors and ambient) in many regions throughout the US and the world. More specifically, woodstoves have been identified as a major source of PM(2.5) in valley locations throughout the Northern Rocky Mountains, where biomass combustion is the predominant source of home heating. In this study, we present results that demonstrate the dramatic reduction in PM(2.5) concentrations (as measured by TSI, Inc. DustTrak PM(2.5) air samplers) inside homes following the replacement of old, polluting woodstove with new EPA-certified woodstoves.

Optimisation of circulating biomarkers of cell death for routine clinical use

BACKGROUND

M30 and M65 enzyme-linked immunosorbent assays detect circulating cytokeratin 18 fragments released during caspase-dependent or total cell death, respectively, and have potential as biomarkers in epithelial cancers. While these assays have been validated, their robustness for routine clinical use is unknown.

PATIENTS AND METHODS

M30 and M65 were measured in matched serum and plasma samples from 31 lung cancer patients and 18 controls.

RESULTS

Time allowable between sample acquisition and processing is critical for assays in clinical use. A 4-h delay in processing at room temperature increased M30 (P < 0.0001), an effect minimised by incubation on ice. M30 and M65 in serum were resistant to processing variations including delays. Serum and plasma measurements correlated well although M30 but not M65 was lower in serum (P < 0.0005). Less variation between duplicate assays was observed in serum. Prolonged storage (-80 degrees C) led to increased M30 (12%, 6 months; 34%, 1 year). Sample dilution in the supplied assay diluent proved non-linear, whereas dilution in donor serum or porcine plasma restored linearity up to a ratio of 1 : 6.

CONCLUSION

We present recommendations that improve the reliability of these assays for clinical use and recommend serum as the preferred matrix with data more resistant to variations in collection.

Molecular characterization of the Fusarium graminearum species complex in Japan

Members of the Fusarium graminearum species complex are important cereal pathogens worldwide and belong to one of at least nine phylogenetically distinct species. We examined 298 strains of the F. graminearum species complex collected from wheat or barley in Japan to determine the species and trichothecene chemotype. Phylogenetic analyses and species-diagnostic polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLPs) revealed the presence and differential distribution of F. graminearum sensu stricto (s. str.) and F. asiaticum in Japan. F. graminearum s. str. is predominant in the north, especially in the Hokkaido area, while F. asiaticum is predominant in southern regions. In the Tohoku area, these species co-occurred. Trichothecene chemotyping of all strains by multiplex PCR revealed significantly different chemotype compositions of these species. All 50 strains of F. graminearum s. str. were of a 15- or 3-acetyl deoxynivalenol type, while 173 (70%) out of 246 strains of F. asiaticum were of a nivalenol type. The possibility of gene flow between the two species was investigated by use of 15 PCR-RFLP markers developed in this study. However, no obvious hybrids were detected from 98 strains examined, including strains collected from regions where both species co-occur.

Physiological noise in near-infrared spectroscopy: implications for optical brain computer interfacing

Near-infrared spectroscopy is a non-invasive optical method used to detect functional activation of the cerebral cortex. Cognitive, visual, auditory and motor tasks are among the functions that have been investigated by this technique in the context of optical brain computer interfacing. In order to determine whether the optical response is due to a stimulus, it is essential to identify and reduce the effects of physiological noise. This paper characterizes noise typically present in optical responses and reports signal processing approaches used to overcome such noise.

Final results of a phase I clinical trial of the bioreductive drug RH1

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Background: RH1 (2,5-diaziridinyl-3-[hydroxymethyl]-6-methyl-1,4-benoquinone) is a novel bioreductive drug which is activated by the two electron reductase, DT-diaphorase (DTD) (NAD(P)H:quinone oxidoreductase). DTD is over-expressed in many tumors relative to normal tissue, especially lung, breast and colorectal tumors, so it is hoped that RH1 is selectively activated in such tumours with minimal normal tissue toxicity. Methods: Under the auspices of the CR-UK Drug Development Office, a dose escalation phase I trial of RH1 was performed at two centres. The primary objective was to establish the maximum tolerated dose (MTD) of RH1 given as a 10–30 minute infusion for 5 days every 3 weeks. Toxicity was assessed according to NCI CTC V2.0 criteria. Secondary objectives were to determine RH1 pharmacokinetics (PK), DNA cross-linking in peripheral blood lymphocytes and tumour cells, DTD activity in tumour, NQO1 polymorphism status and document any anti-tumour activity. Results: Eighteen patients of WHO performance status 0–1 with advanced refractory solid malignancies were enrolled. 14 patients were male and eight patients had colorectal adenocarcinoma. The MTD was 1,430 mcg/m2/day and the dose-limiting toxicity (DLT) was bone marrow suppression. DLT occurred in both patients treated at 1,905 mcg/m2/day: one developed grade 3 thrombocytopenia with haemorrhage and grade 3 anaemia; the other died from neutropenic sepsis. Other clinically significant drug-related toxicities included moderate phlebitis and fatigue. Plasma PK analysis on days 1 and 5 in cycle 1 showed rapid plasma clearance of RH1 (t1/2=12.3 mins) with AUC increasing proportionately with dose. The comet-X assay showed increases in DNA inter-stand cross-linking in peripheral blood lymphocytes treated at 200 mcg/m2/day or above. These cross-links were detectable within one hour of commencement of dosing and reached a maximum of 30%. DNA cross-linking after RH1 was seen in tumour samples, even with low levels of DTD. One patient was homozygous for the NQO1 polymorphism. No objective tumour responses were recorded. Conclusions: The MTD of 1,430 mcg/m2/day is the dose recommended for phase II clinical trials. Tested doses were associated with DNA cross-linking in both peripheral blood lymphocytes and tumour cells.

No significant financial relationships to disclose.

Medical applications of terahertz imaging: a review of current technology and potential applications in biomedical engineering

Terahertz (THz) imaging is in its early stages of development but already the potential clinical impact of this new imaging modality is clear. From cancer research to DNA analysis THz technology is improving or even making possible imaging of hitherto inaccessible phenomena. In this paper we present a short review of THz imaging from the point of view of biomedical engineering. We discuss the current state of the art in terms of THz imaging systems; describe current applications, future potential and our own approaches to harnessing this novel technology. We draw attention to open problems in the area with respect to the limitations of the technology before concluding with descriptions of our future work in the area.

No deterioration of kinematics and cruciate function 10 years after medial unicompartmental arthroplasty

The mechanisms of failure for unicompartmental arthroplasty are poorly understood. There is some suggestion that long term ligament degeneration, particularly of the anterior cruciate ligament (ACL), may affect long term survivorship. This study evaluated whether the cruciate mechanism remained functional in the long term (10 years) following UKA. Two separate cohorts of patients who had undergone St Georg Sled medial compartmental arthroplasty had knee kinematics assessed using an established fluoroscopic technique. One group (early) was assessed at a mean of 46 months (3.8 years) since surgery, whilst the other (late) was assessed at a mean of 125 months (10.4) following surgery. No significant difference was found in the sagittal plane kinematics between the two groups or in comparison to the control normal knee. The results suggest that after fixed bearing UKA the cruciate mechanism remains intact over time and the ligaments continue to function similarly to those of the normal knee.