Gene Copy Number Amplification Research Articles

Abstract 3920: Understanding the molecular nature of cancer cell lines

Abstract Large-scale cancer genome programs have generated rich data of genetic abnormalities observed in thousands of clinical patient tumors, which provides a major opportunity to develop a landscape of molecular aberrations across tumor types and propose new therapeutic targets. Although human tumor cell lines have been important tools for the cancer researcher for decades, there is a lack of bio-functional validation of genetic alterations and systematic molecular characterization across commonly used cell lines in this genomic age. To meet the need of applying cancer genome knowledge to facilitate basic and translational cancer research, an updated and accurate knowledge of the cell lines in use, particularly from a molecular viewpoint, is critical for in vitro studies. Here, we show systematic molecular characterization and clustering of 90 authenticated human tumor cell lines, which represent the most common human cancer types found in the clinic, such as lung, breast, colon, pancreatic, skin cancer and so on. By next generation sequencing and molecular profiling, those tumor cell lines were fully analyzed to capture the driver gene mutations, DNA copy number variations, gene expressions, protein expressions and relevant cell signaling pathway activations. In addition to driver mutations such as BRAF V600, KRAS G12, PI3K E545 and EGFR T790, the gene copy number amplifications of AKT, FGFR, MET, ERBB2 and deletion of PTEN are presented in this work. Moreover, correlating with the verified genetic alternations, the endogenous basal levels of protein expression and signaling pathway activations within the cells were analyzed by western blot and immunofluorescence staining. A set of 6 wild type control cell lines that were derived from either normal tissues or tumors were characterized in parallel. Furthermore, live cell growth kinetics was continually monitored by label-free cell based assay. Finally, the cell lines are clustered into 10 genetic alteration panels according to driver genes, critical protein kinases, or key components of signaling pathways. Cell lines are essential models for progressing our understanding of the cancer genome, as they allow for the functional and biological validation of the genetic alterations proposed by NGS data. The genetic alteration tumor cell panels and their molecular signature profiles provide powerful tools to accelerate the discoveries in basic cancer research, compound screening, biomarker selection, pathway analysis, and targeted therapeutic development. Citation Format: Lysa A. Volpe, Anupreet Bal, John Foulke, Michael Jackson, Luping Chen, Fang Tian. Understanding the molecular nature of cancer cell lines. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3920. doi:10.1158/1538-7445.AM2014-3920

Absence of amplification of the FGFR1-gene in human malignant mesothelioma of the pleura: a pilot study.

BackgroundMesothelioma (MPM) is a rare malignant disease with a worse outcome. Fibroblast growth factor 1 (FGFR1) may be an interesting target for selective tyrosine kinases inhibitors (TKI) in MPM. The aim of this study was to evaluate the amplification of the FGFR1 gene in patients suffering from MPM.FindingsWe identified nineteen male patients treated in our department between August 2008 and July 2010 matching the inclusion criteria. Mean age was 68 years. Histopathological examination confirmed thirteen patients with epitheloid subtype, five with biphasic and one patient with sarcomatoid. Fluorescence in situ hybridization analysis revealed no polysomy nor an amplification of the FGFR gene copy number in any case.ConclusionRegarding that also EGFR amplifications in MPM are absolute rarities, our findings may be a hint that TKI’s will not satisfy the hope for a new era in the treatment of MPM.

Novel PAK4 inhibitors for pancreatic cancer therapy.

233 Background: Pancreatic cancer (PC) is a deadly disease in urgent need of novel molecularly targeted drugs. Gene copy number amplification studies in PC patient cohorts has shown amplification of the p21-activated kinase (PAK) family member PAK4. PAK4 acts as a key effector of the Rho family GTPases downstream of Ras signaling. Moreover, PAK4 protein is over-expressed in PC cell lines but not in normal human pancreatic ductal epithelial (HPDE) cells. Most importantly, RNA interference of PAK4 has been shown to suppress PC cell proliferation. These studies clearly make PAK4 an attractive therapeutic target especially because direct targeting of Kras has been a failure. Methods: We have identified a new class of PAK4 allosteric modulators that show anti-proliferative activity against several PC cell lines (IC50s <250nM) while sparing normal HPDE (IC50s5 fold higher). Results: Cell growth inhibition is concurrent with apoptosis induction and suppression of colony formation in the PC cell lines (and not in HPDE cells). Our small molecule PAK4 allosteric modulator, KPT-7189, suppresses PAK4 protein expression and caused reversal of anti-apoptotic signaling. PAK4 RNA interference enhances KPT-7189 activity, and co-immunoprecipitation experiments showed disruption of PAK4 binding partners. KPT-7189 also inhibited spheroid forming ability of highly resistant PC cells carrying markers of cancer stem cells (CSCs;triple positive for CD33+CD44+EpCAM+) consistent with epithelial-to-mesenchymal (EMT) phenotype. Molecular analyses of KPT-7189 treated CD33+CD44+EpCAM+ spheroids showed suppression of EMT and CSC markers with re-expression of epithelial phenotype markers. Another potent PAK allosteric modulator in the same series, KPT-7651 showing good oral bioavailability (%F = 95%) was well tolerated by mice with a maximum tolerated dose of 60 mg/kg following oral administration. Pre-clinical animal efficacy trial in sub-cutaneous, orthotopic and LSL-KrasG12D/+;LSL-Trp53R172H/+;Pdx-1-Cre transgenic mice model is currently under investigation. Conclusions: This is the first proof of concept study demonstrating the development of a PAK4-targeted drug for the treatment of PC, and thus further pre-clinical and clinical investigations are warranted.

ALK gene amplification is associated with poor prognosis in colorectal carcinoma

Background:Recently, the anaplastic lymphoma kinase (ALK) has been found to be altered in several solid and haematological tumours. ALK gene copy number changes and mutations in colorectal cancers (CRCs) are not well characterised. We aimed to study the prevalence of ALK copy number changes, translocations, gene mutations and protein expression in 770 CRC patients, and correlate these findings with molecular and clinico-pathological data.Methods:ALK gene copy number variations and ALK expression were evaluated by fluorescence in situ hybridisation (FISH) and immunohistochemistry, respectively.Results:Translocations of the ALK gene were not observed; 3.4% (26 out of 756) of the CRC patients tested had an increase in ALK gene copy number either amplification or gain. Interestingly, increased ALK gene copy number alteration was associated with poor prognosis (P=0.0135) and was an independent prognostic marker in multivariate Cox proportional hazards model. The study reveals a significant impact of ALK gene copy number alterations on the outcome of patients with CRC.Conclusion:The findings of our study highlight a potential role of targeting ALK in advanced CRCs by using ALK FISH and ALK IHC as a screening tool to detect ALK alterations. Based on these findings, a potential role of ALK inhibitor as a therapeutic agent in a subset of CRC merits further investigation.

Overexpression and promoter mutation of the TERT gene in malignant pleural mesothelioma

Malignant pleural mesothelioma (MPM) is a very aggressive tumor with no known curative treatment. Better knowledge of the molecular mechanisms of mesothelial carcinogenesis is required to develop new therapeutic strategies. MPM, like all cancer cells, needs to maintain telomere length to prevent senescence. Previous studies suggested that the telomere lengthening mechanism in MPM is based mainly on telomerase activity. For this reason, we focused on the key catalytic enzyme, TERT (telomerase reverse transcriptase), by analyzing its gene expression in MPM and by studying the mechanism underlying its upregulation. We used our large collection of MPM composed of 61 MPM in culture and 71 frozen MPM tumor samples. Evaluation of TERT mRNA expression by quantitative RT-PCR showed overexpression in MPM in culture compared with normal mesothelial cells, and in MPM tumor samples compared with normal pleura. We identified a 'hot spot' of mutations in the TERT gene core promoter in both MPM in culture and in MPM tumor samples with an overall frequency of 15%. Furthermore, data clearly identified mutation in the TERT promoter as a mechanism of TERT mRNA upregulation in MPM. In contrast, gene copy number amplification was not associated with TERT overexpression. Then, we analyzed the clinicopathological, etiological and genetic characteristics of MPM with mutations in the TERT promoter. TERT promoter mutations were more frequent in MPM with sarcomatoid histologic subtype (P<0.01), and they were frequently associated with CDKN2A gene inactivation (P=0.03). In conclusion, a subgroup of MPM presents TERT promoter mutations, which lead to TERT mRNA upregulation. This is the first recurrent gain-of-function oncogenic mutations identified in MPM.

Fibroblast growth factor receptor 1 (FGFR1) copy number is an independent prognostic factor in non-small cell lung cancer

Fibroblast growth factor receptor 1 (FGFR1) is an oncogene that can potentially be targeted by tyrosine kinase inhibitors. We aimed to investigate the prevalence and prognostic significance of alterations in FGFR1 copy number in non-small cell lung cancer (NSCLC). FGFR1 status was evaluated by chromogenic silver in situ hybridisation (ISH) in tissue microarray sections from a retrospective cohort of 304 surgically resected NSCLCs and results were correlated with the clinicopathological features and overall survival. High FGFR1 gene copy number (amplification or high-level polysomy) was significantly more frequent in squamous cell carcinomas (SCC) (24.8%) and large cell carcinomas (LCC) (25%) compared to adenocarcinomas (11.3%) (p=0.01 and p=0.03 respectively). Among NSCLC there was no significant correlation between FGFR1-positive status and other clinicopathological features including age, gender, smoking history, tumour size, lymph node status, stage, grade, vascular, lymphatic or perineural invasion. FGFR1-positive patients showed a tendency to longer overall survival in univariate analysis (p=0.14). Multivariate survival analysis using Cox regression model confirmed FGFR1-positive patients had a significant reduction in the risk of death compared to FGFR1-negative patients (HR 0.6; p=0.02). High FGFR1 gene copy number is a common finding in SCC and LCC and is an independent favourable prognostic factor.

Screening for EGFR Amplifications with a Novel Method and Their Significance for the Outcome of Glioblastoma Patients

Glioblastoma is a highly aggressive tumour of the central nervous system, characterised by poor prognosis irrespective of the applied treatment. The aim of our study was to analyse whether the molecular markers of glioblastoma (i.e. TP53 and IDH1 mutations, CDKN2A deletion, EGFR amplification, chromosome 7 polysomy and EGFRvIII expression) could be associated with distinct prognosis and/or response to the therapy. Moreover, we describe a method which allows for a reliable, as well as time- and cost-effective, screening for EGFR amplification and chromosome 7 polysomy with quantitative Real-Time PCR at DNA level. In the clinical data, only the patient’s age had prognostic significance (continuous: HR = 1.04; p<0.01). At the molecular level, EGFRvIII expression was associated with a better prognosis (HR = 0.37; p = 0.04). Intriguingly, EGFR amplification was associated with a worse outcome in younger patients (HR = 3.75; p<0.01) and in patients treated with radiotherapy (HR = 2.71; p = 0.03). We did not observe any difference between the patients with the amplification treated with radiotherapy and the patients without such a treatment. Next, EGFR amplification was related to a better prognosis in combination with the homozygous CDKN2A deletion (HR = 0.12; p = 0.01), but to a poorer prognosis in combination with chromosome 7 polysomy (HR = 14.88; p = 0.01). Importantly, the results emphasise the necessity to distinguish both mechanisms of the increased EGFR gene copy number (amplification and polysomy). To conclude, although the data presented here require validation in different groups of patients, they strongly advocate the consideration of the patient’s tumour molecular characteristics in the selection of the therapy.

Prognostic role of MET expression in early stage NSCLC.

7567 Background: The MET receptor tyrosine kinase and its ligand are associated with the malignant phenotype. In non-small cell lung cancer (NSCLC) MET expression increases with disease stage and is involved in de novo and acquired resistance to tyrosine kinase inhibitors. Despite this, in early stage NSCLC small data series have failed to demonstrate MET expression to be prognostic. We investigated a large cohort of patients who underwent curative surgical resection at our institution to determine whether MET receptor or gene amplification was prognostic. Methods: Tissue Microarrays (TMAs) were constructed using 1mm cores of FFPE primary NSCLC tissues in triplicate. TMAs were stained with the SP44 clone (Novus Biologicals) and a H-score calculated based on % cells stained and intensity; (%cellsx1)+(%cellsx2)+(%cellsx3) with a minimum of 0 and maximum of 300. The mean of triplicate values was calculated. MET gene amplification was detected using Ventana’s MET DNP probe with ultraView SISH DNP silver detection, performed on Ventana’s XT autostainer. DNA was isolated and subjected to mutational profiling using Sequenom’s LungCarta panel. Results: Data for 508 patients, 352 (69%) male, were available for analysis including 329 pathological node negative (pN0), 67 pN1, 104 pN2 and 8 patients with resected primaries and solitary brain metastases (M1). Most patients were smokers with only 33 (6%) non-smokers. The median MET H-score was 100 and consistent across N0, N1 and N2 patients, although was higher in M1 patients. Median H-scores were significantly higher in adenocarcinoma compared to squamous cell carcinoma (140 vs 91.5, p&lt;0.0001). Increased MET expression (H-score&gt;100) was seen in 227 (45%) patients and associated with significantly improved overall survival (HR 1.28 95% CI 1.04-1.59; p=0.023). In univariate analyses improved survival occurred in all stages and histologies. DNA and multivariate analyses are pending. MET gene copy number amplification was detected in 11 cases. Conclusions: In contradistinction to advanced NSCLC, increased MET receptor expression is associated with improved survival in a large cohort of early stage lung cancer. Further correlation with mutation status and gene rearrangements will be reported.

Abstract 928: Volitinib (HMPL504), a novel, selective and potent cMET inhibitor, is efficacious in primary tumor models of cMET-driven gastric cancer.

Abstract Gastric cancer (GC) incidence rates are amongst the highest in Asian countries including; China, Japan and Korea(1). 5-year survival rates in early stage disease have improved through aggressive combinations of surgery and chemo/radiotherapy. In late stage disease however, despite Her2 molecular segmentation and trastuzumab therapy, prognosis remains dismal and novel therapeutic options are urgently required(2). The MET oncogene encodes the receptor tyrosine kinase for hepatocyte growth factor and controls genetic programs leading to cell growth, invasion and survival. Dysregulation of MET signaling is a common feature of a diverse range of human tumor types and thus represents a highly competitive and attractive therapeutic target. Volitinib (HMPL-504) is an orally bioavailable, highly selective and potent small molecule ATP-competitive inhibitor, which inhibits cMET autophosphorylation and downstream signaling (3). Volitinib is currently in Phase I clinical development. To evaluate the utility of volitinib in treating patients with GC, we established the incidence of cMET amplification and overexpression and attempted to correlate this with response to volitinib in primary GC tumor models. Elevated cMET gene copy number (amplification 5%, high polysomy 13%), and protein overexpression (12%, cases &amp;gt; IHC 2+, 16% &amp;gt; IHC1+) were detected in a cohort of 217 Chinese GC samples using fluorescent in situ hybridization (FISH) and immunohistochemical (IHC) approaches. In vitro proliferation assays were performed on a panel of 26 GC cell lines and profound sensitivity to volitinib was demonstrated in lines harboring elevated cMET gene copy number (GI50 range 6 to 49nM). In the cMET amplified GC xenograft model, Hs746t, once-daily oral dosing of volitinib (2.5mg/kg) elicited potent anti-tumour activity at well-tolerated doses (97% tumour growth inhibition after 16 days dosing, P&amp;lt;0.0001) which correlated well with pharmacodynamic modulation of phospho-cMET signaling. To strengthen the translational relevance of these data, a panel of cMET amplified primary GC models were identified and established. In these models, volitinib demonstrated potent tumor growth inhibition or regressions (90% and 84% TGI at 10mg/kg/qd, all P&amp;lt;0.0001), correlated with pharmacodynamic modulation of tumor phospho-cMET. In contrast, 10mg/kg/qd volitinib was inactive (18% TGI, P=0.2405) in a cMET non-amplified control model. We also evaluated the activity of volitinib in combination with docetaxel, a standard of care chemotherapeutic commonly used in the treatment of gastric cancer. In model Hs746t, volitinib demonstrated additive benefit when used with docetaxel at well tolerated doses. These data support the potential clinical utility of volitinib as a selective agent for the therapeutic treatment of gastric cancers harboring dysregulated cMET signaling. Citation Format: Paul R. Gavine, Shiming Fan, Haihua Fu, Lu Han, Yuan Jie Liu, Jing Lv, Weiguo Qing, Yongxin Ren, Weiguo Su, Xinying Su, Huiying Wang, Liang Xie, Shirlian Xu, Wen Xu, XiaoLu Yin, Yongjuan Yu, Tianwei Zhang, Q.May Wang. Volitinib (HMPL504), a novel, selective and potent cMET inhibitor, is efficacious in primary tumor models of cMET-driven gastric cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 928. doi:10.1158/1538-7445.AM2013-928

Abstract 2390: EGFR variant III act as the major determinant factors in the EGFR/PI3K/AKT pathway for the survival outcome of oral cancer patients.

Abstract Background: Activation of the EGFR/PI3K/AKT pathway is known for the crucial role in tumorigenesis of oral cancer. Our study focused to analyze the aberrations of the regulatory factors which lead to over-activation of this pathway. Patients and methods: A series of studies was conducted with application of the archival oral cancer tissue specimens which was obtained from patients who received surgical resection. For the factors in interest, we studied their protein expression and gene copy number (GCN) by immunohistochemical staining and real-time polymerase chain reaction, respectively. Statistical assessment was then arranged to determine their association and the impact to survival outcomes. Results: In the total108 samples examined, the activation of AKT was evidenced in 86.9% by identification of the cytoplasmic phosphorylated AKT (pAKT). There were 63.9% of the samples with expression of membranous wild-type EGFR, and 49.1% of the samples with undetectable PTEN in the tumor tissue. Judgment of EGFR variant III (EGFRvIII) showed that 75.0% of the samples were positive, with 38.5% low expression and the remaining 31.5% high expression. Studies of the PIK3CA gene revealed alteration of GCN in 24.8% of the samples and hotspot point mutation in 2.3% of the samples. Those of the EGFR gene showed evidence of GCN amplification in 49.0% of the samples, and were in association to expression of the wild-type protein but not EGFRvIII. Further analysis of EGFRvIII negative/low or high expression was in correlation to the T classification and the disease stage. For the survival analyses, classification according to pAKT or EGFRvIII both led to significantly different Kaplan-Meier curves. Moreover, simultaneous judgment by the status of EGFR wild type and variant III also served to predict the patient survival. By the multivariate analysis, individual factors such as pAKT, EGFRvIII and the disease stage were further suggested as the determinants of the survival outcome. Conclusions: Our investigation showed that in oral cancers, aberrations in the regulatory factors of the AKT pathway were frequent. Expression of EGFRvIII and pAKT were negative predictors for the patient survival. (The work was supported by the Department of Health, Executive Yuan, Taiwan [DOH101-TD-C-111-004] and by the National Health Research Institutes, Taiwan [CA-101-PP-09]) Citation Format: Kwang-yu Chang, Shan-Yin Tsai, Shang-Hung Chen, Hsiao-Hui Tsou, Chia-Jui Yen, Careen K. Tang, Ching-Yu Yen, Jang-Yang Chang. EGFR variant III act as the major determinant factors in the EGFR/PI3K/AKT pathway for the survival outcome of oral cancer patients. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2390. doi:10.1158/1538-7445.AM2013-2390

Changes in MYCN expression in human neuroblastoma cell lines following cisplatin treatment may not be related to MYCN copy numbers

Neuroblastoma is a tumor accounting for approximately 10% of all childhood malignancies and 50% of all childhood cancer-related deaths. MYCN gene copy number variation represents the most important prognostic factor in neuroblastoma. Prognostic significance of MYCN gene expression is more complicated and may depend on other factors such as MYCN gene copy number status. In the present study, we assessed MYCN gene expression using real-time RT-PCR following cisplatin treatment in three human neuroblastoma cell lines (UKF-NB-3, UKF-NB-4 and SK-N-AS) and their cisplatin-resistant counterparts. We also examined MYCN gene status and copy number (gain and amplification) variations using interphase and metaphase fluorescent insitu hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA). Only cisplatin-sensitive UKF-NB-4 cells exhibited decreased MYCN expression following treatment with cisplatin. Other sensitive neuroblastoma cells did not exhibit a change in MYCN expression. In contrast, cisplatin-resistant UKF-NB-4 and SK-N-AS cells exhibited increased MYCN expression irrespective of the number of MYCN copies or concentration of cisplatin in the medium. In MYCN-amplified neuroblastoma cells we did not observe any significant change in the number of MYCN copies after cisplatin treatment, whereas MYCN-non-amplified SK-N-AS cells revealed during cisplatin treatment an increased number of MYCN gene copies caused by 2p gain in the majority of cells by FISH. We postulated that cisplatin treatment does not result directly in altered transcription of MYCN. A functional change in MYCN mRNA levels and increased MYCN expression in cisplatin-resistant neuroblastoma cells do not have a clear relationship to MYCN copy numbers. These findings may further contribute to the understanding of cisplatin chemotherapy in connection with MYCN expression, and the possible copy number variations in MYCN neuroblastoma cells may be of importance since targeting of MYCN is being tested as neuroblastoma therapy.

Copy number variations of the F8 gene are associated with venous thromboembolism

Venous thromboembolism (VTE) is a complex disease and several inherited and acquired factors are relevant to its occurrence. Among these, an elevated level of plasma coagulation factor VIII (FVIII) is an established risk factor for VTE; copy number variations (CNVs) have also been discovered to be associated with many diseases. To explore the proposed association between CNV of the F8 gene and the risk of VTE. A case-control study including 179 VTE patients and 176 healthy individuals were enrolled in this study. Activity of plasma factor VIII was measured. Genomic DNA was extracted for subsequent quantitative real-time PCR analysis of CNVs of the F8 gene. Plasma factor VIII levels were significantly higher in VTE patients than in healthy controls (251% vs. 99%, p<0.01). Copy number of the F8 gene in VTE patients was significantly higher than in healthy controls. (male: p=6.1×10(-14), OR=12, 95%CI: 6.0-25; female: p=4.3×10(-10), OR=9.5, 95%CI: 4.5-20). Plasma factor VIII levels in the samples with high copies of the F8 gene were higher than in those individuals with normal copy number (male: p=0.023; female: p=0.036). Amplification of the F8 gene copy number seems to enhance factor VIII activity and was associated with VTE.

FGFR1 Copy number is an independent prognostic factor in non-small cell lung cancer

<h3>Aim</h3> <i>Fibroblast growth factor receptor 1</i> (<i>FGFR1</i>) is an oncogene that can potentially be targeted by tyrosine kinase inhibitors. We aimed to investigate the prevalence and prognostic significance of alterations in <i>FGFR1</i> copy number in non-small cell lung cancer (NSCLC). <h3>Methods</h3> <i>FGFR1</i> status was evaluated by chromogenic silver <i>in situ</i> hybridisation (ISH) in tissue microarray sections from a retrospective cohort of 263 surgically resected NSCLCs and results were compared to clinicopathological features and patient survival. <h3>Results</h3> <i>FGFR1</i> ISH results were obtained in 221 cases. High <i>FGFR1</i> gene copy number (amplification or high-level polysomy) was significantly more frequent in squamous cell carcinomas (SCC; 24.4%) and large cell carcinomas (LCC; 26.2%) compared to adenocarcinomas (9.2%) (<i>p</i>=0.009 and <i>p</i>=0.016, respectively). There was no significant correlation between <i>FGFR1</i> positive status and other clinicopathological features including age, gender, smoking history, tumour size, lymph node status, stage, grade, vascular, lymphatic or perineural invasion. <i>FGFR1</i> positive patients showed a tendency to longer overall survival in univariate analysis (<i>p</i>=0.14). Multivariate survival confirmed <i>FGFR1</i> positive patients had a significant reduction in the risk of death compared to <i>FGFR1</i> negative patients (HR 1.61; <i>p</i>=0.025). <h3>Discussion</h3> <i>FGFR1</i> gene copy number is frequently increased in SCC and LCC and is an independent favourable prognostic factor.

Abstract 1737: Co-existence of positive MET FISH status with EGFR mutations signifies poor prognosis in lung adenocarcinoma

Abstract MET, which is located in 7q31, is a receptor tyrosine kinase for hepatocyte growth factor. Overexpression of MET has been reported in various malignancies and is associated with cell proliferation, inhibition of apoptosis, and metastasis. MET amplification has been reported to contribute to acquired resistance to epidermal growth factor tyrosine kinase inhibitors (EGFR-TKI) in non-small cell lung cancer(NSCLC), being observed among 5-10% of those patients. Therefore, MET gene alterations could be both prognostic and predictive. To evaluate MET gene copy number, fluorescence in situ hybridization (FISH), real-time PCR, and comparative genomic hybridization (CGH) have been used. The results of real-time PCR do not directly reflect cancer cells. CGH is not suitable for the evaluation of a large number of specimens due to cost. Therefore, FISH is the most practical method for evaluation of MET gene copy number. However, the frequency of positive cases varies due to a lack of standardized criteria. We evaluated MET gene copy number in lung adenocarcinoma and its association with clinicopathological characteristics. FISH was applied to evaluate high MET gene copy number and true amplification in 138 lung adenocarcinoma patients using two criteria: the Cappuzzo scoring system and PathVysion. MET positive cases according to the Cappuzzo scoring system evidenced both aneuploidy and true amplification, whereas PathVysion revealed only amplification. Proportion of MET FISH positive cases was 15% and 4% determined by the Cappuzzo system and PathVysion, respectively. PathVysion demonstrated higher frequencies of MET FISH positives among men and smokers and evidenced no MET FISH positives in patients with bronchioloalveolar carcinoma, which is recognized as pure lepidic growth without invasion of stroma, blood vessels, or pleura. Prognosis was significantly associated with MET FISH positive only as defined by the PathVysion system (gene amplification), not by the Cappuzzo system. However, progression-free survival time of patients with both EGFR mutations and MET FISH positive defined by the Cappuzzo scoring system was significantly shorter than with EGFR mutations alone. These results suggest that MET FISH is a potential prognostic factor and co-existence of EGFR mutation and MET FISH positive status evidences poorer prognosis compared to EGFR mutation alone, which is consistent with the results of in vitro experiments. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1737. doi:1538-7445.AM2012-1737

EGFR, HER2, survivin, and loss of pSTAT3 characterize high-grade malignancy in salivary gland cancer with impact on prognosis

Increased gene copy number (high polysomy or amplification) of EGFR and HER2 has evolved as a predictor for response to targeted therapy. STAT3 and the apoptosis inhibitor survivin represent distinct oncogenes in various human neoplasms. The purpose of this study was to evaluate protein and gene status of these biomarkers by immunohistochemistry and dual color fluorescence in situ hybridization on tissue microarrays of 286 salivary gland carcinomas in the context of clinical and histopathologic characteristics. Diverse tumor types showed overexpression and increased gene copy number of EGFR and HER2. Amplification of HER2 was found in 35.5% of salivary duct carcinomas. Protein overexpression was strongly associated with high gene copy number for both EGFR and HER2 (P < .001). Overexpression and increased gene copy number of EGFR and HER2 were correlated to high-grade malignancy (P < .001) and unfavorable prognosis (P < .001). Strong nuclear staining of survivin was found in 18.9% of tumors and was associated with high-grade malignancy (P < .001), overexpression, and high gene copy number of EGFR and HER2 (P ≤ .05) as well as unfavorable prognosis (P < .001). Overexpression of nuclear pSTAT3 was found in 28.3% of tumors and correlated with well tumor differentiation (P < .001) and favorable prognosis (P = .001). Loss or weak expression of pSTAT3 was inversely associated with overexpression of survivin (P < .001) as well as overexpression and high gene copy number of EGFR and HER2 (P < .05). Overall, overexpression and increased gene copy number of EGFR and HER2 characterize high-grade malignancy with unfavorable prognosis in salivary gland cancer. Nuclear survivin typifies aggressive tumors with worse prognosis, whereas nuclear pSTAT3 might play a role as a tumor suppressor in absence of EGFR, HER2, and survivin.

Co-existence of positive MET FISH status with EGFR mutations signifies poor prognosis in lung adenocarcinoma patients

MET, a receptor tyrosine kinase for hepatocyte growth factor, is associated with tumor progression and acquired resistance to epidermal growth factor tyrosine kinase inhibitors (EGFR-TKI). Therefore, MET gene alterations could be both prognostic and predictive. Fluorescence in situ hybridization (FISH) is one method for assessing gene alteration, but the frequency of positive cases varies due to a lack of standardized criteria. We evaluated MET gene copy number in lung adenocarcinoma and its association with clinicopathological characteristics. FISH was applied to evaluate high MET gene copy number and true amplification in 138 lung adenocarcinoma patients using two criteria: the Cappuzzo scoring system and PathVysion. MET positive cases according to the Cappuzzo scoring system evidenced both aneuploidy and true amplification, whereas PathVysion revealed only amplification. Proportion of MET FISH positive cases was 15% and 4% determined by the Cappuzzo system and PathVysion, respectively. PathVysion demonstrated higher frequencies of MET FISH positives among men and smokers and evidenced no MET FISH positives in patients with bronchioloalveolar carcinoma. Prognosis was significantly associated with MET FISH positive only as defined by the PathVysion system (gene amplification), not by the Cappuzzo system. However, progression-free survival time of patients with both EGFR mutations and MET FISH positive defined by the Cappuzzo scoring system was significantly shorter than with EGFR mutations alone. These results suggest that MET FISH is a potential prognostic factor and coexistence of MET FISH with EGFR mutations signifies worse prognosis.

Clinical significance of genetic alterations and expression of epidermal growth factor receptor (EGFR) in head and neck squamous cell carcinomas

The significance of epidermal growth factor receptor (EGFR) signaling is well studied in a number of different tumors, but limited data is available with regard to head and neck squamous cell carcinoma (HNSCC). Since anti-EGFR therapies are currently under investigation in these malignancies as well, comprehensive information about the alteration of EGFR in HNSCC is necessary to design the most appropriate therapeutic protocols. We examined retrospectively the gene copy number of EGFR by FISH and the protein expression by immunohistochemistry using different epitope-specific antibodies in paraffin-embedded primary tumors of five different regions, from 71 HNSCC patients who had not been treated with anti-EGFR therapy. In seven cases corresponding lymph node metastases were also available for comparative analyses. We also determined the mutational status of tyrosine kinase (TK) domain (exon 19 and 21) and the extracellular deletion mutation (vIII) of EGFR, the KRAS mutation at codon 12 and the presence of HPV infection. Eight of the 71 cases (11.3%) showed EGFR gene amplification (most of them localized into the hypopharyngeal region) and the increased gene copy number (amplification+polysomy) was 43.7%. Despite pronounced intratumoral heterogeneity of EGFR protein expression being found, the high EGFR expression correlated with poor prognosis. On the other hand, the phosphorylation of EGFR was associated with prolonged survival. No mutations in the TK domain of EGFR were found in any of the HNSCC patients and only two cases were KRAS mutant at codon 12. We detected vIII deletion mutation of EGFR in 21% of the samples, but there was no statistically significant correlation between the presence of vIII mutant form and patient survival. EGFR vIII mutation was, however, associated with increased gene copy number. Fourteen of 71 cases (19.7%) were HPV-positive and the incidence of infection showed a decreasing tendency from the oral cavity towards the larynx. Interestingly, in contrast to previous findings, we could not observe improved survival in HPV-positive patients compared to non-infected patients, most probably due to the fact that the majority of these HNSCC patients were smokers and alcohol consumers. In conclusion, we found that increased EGFR protein levels and gene copy numbers (not gene amplification alone) have prognostic significance in the investigated HNSCC patient population. However, the relatively high incidence of the EGFR-vIII mutant form warrants careful therapeutic decision-making when choosing between different anti-EGFR treatment options.

Contribution of Gene Amplification to Evolution of Increased Antibiotic Resistance inSalmonella typhimurium

The use of beta-lactam antibiotics has led to the evolution and global spread of a variety of resistance mechanisms, including beta-lactamases, a group of enzymes that degrade the beta-lactam ring. The evolution of increased beta-lactam resistance was studied by exposing independent lineages of Salmonella typhimurium to progressive increases in cephalosporin concentration. Each lineage carried a beta-lactamase gene (bla(TEM-1)) that provided very low resistance. In most lineages, the initial response to selection was an amplification of the bla(TEM-1) gene copy number. Amplification was followed in some lineages by mutations (envZ, cpxA, or nmpC) that reduced expression of the uptake functions, the OmpC, OmpD, and OmpF porins. The initial resistance provided by bla(TEM-1) amplification allowed the population to expand sufficiently to realize rare secondary point mutations. Mathematical modeling showed that amplification often is likely to be the initial response because events that duplicate or further amplify a gene are much more frequent than point mutations. These models show the importance of the population size to appearance of later point mutations. Transient gene amplification is likely to be a common initial mechanism and an intermediate in stable adaptive improvement. If later point mutations (allowed by amplification) provide sufficient adaptive improvement, the amplification may be lost.

Genomic imbalances in Schistosoma-associated and non– Schistosoma-associated bladder carcinoma. An array comparative genomic hybridization analysis

Carcinoma of the urinary bladder is the most common malignancy in many tropical and subtropical countries due to endemic infection by Schistosoma hematobium (bilharzia). In the current study, we performed a high-resolution analysis of gene copy number amplifications using array comparative genomic hybridization to compare DNA copy number changes in pools of Schistosoma-associated (SA) and non– Schistosoma-associated (NSA) bladder cancer (BC). Many DNA copy number changes were detected in all studies, with multiple gains and losses of genetic material. The most frequent alterations were gains on 5p15.2∼p15.33, 8q13.1, and 11q13, and losses on 8p21.3∼p22 and 22q13. Even when SA pools showed no Schistosoma-specific gene copy number profiling as compared to NSA pools, some genes seemed to be gained ( ELN on 7q11.23) and some lost ( PRKAG3 on 2q35 and PRDM6 on 5q23.2) in SA-SCC. The following genes were gained in all histopathologic categories: SRC (20q11.23), CEBPB (20q13.13), and GPR9 (Xq13.1). Our study did not provide clear evidence of differences in carcinogenesis of SA-BC and NSA-BC.

ITARGET: A phase II trial to assess the response to gefitinib in epidermal growth factor receptor (EGFR)-mutated non-small cell lung cancer (NSCLC) tumors

7504 Background: Somatic EGFR mutations correlate with increased response and survival in NSCLC patients (pts) treated with gefitinib. We conducted the 1st prospective US trial of 1st-line gefitinib in pts with advanced NSCLC harboring EGFR mutations. Methods: Chemotherapy-naïve pts with stage IIIB with effusion or IV NSCLC, measurable disease, and = 1 characteristic associated with mutations (female (F), adenocarcinoma (AC), never-smoking (NS), East Asian (EA)) underwent direct DNA sequencing of tumor tissue EGFR exons 18–24. Mutation-positive pts received gefitinib (250 mg/d) until progression or unacceptable toxicity. The primary outcome was response rate (RR) by RECIST criteria. Results: We sequenced 98 pts and detected EGFR mutations in 34 (35%); 3 were not assessable. Observed mutations were 18 (53%) exon 19 deletions (del), 9 (26%) L858R, 3 (9%) exon 20 insertions (ins), 2 T790M/L858R, 1 G719A, and 1 L861Q. Characteristics of the 98 screened pts were 69 F, 89 AC, 37 NS, and 5 EA; those of the 34 mutation pts were 20 (59%) F, 31 (91%) AC, 19 (56%) NS and 2 (6%) EA. The best predictor of EGFR mutation was NS. Of the 34 mutation pts, 31 (91%) received gefinitib. Reasons for non-treatment were pt preference (1 exon 19 del) and mutation associated with gefitinib-resistance (1 T790M/L858R, 1 exon 20 ins). Adverse events were mainly grade 1–2 rash and diarrhea; 1 case of grade 4 interstitial lung disease occurred after 2 weeks of therapy. The RR was 58% (95% confidence interval 39–75) and was 78% in L858R pts and 65% in del 19 pts. There were no responses among the G719A, L861Q, T790M/L858R and exon 20 ins pts treated. 12 pts have progressed, 18 remain on therapy. The median progression-free survival (PFS) is currently 11.8 mo and does not differ by mutation type, though follow-up is short (median 6.8 mo, range 1–24). 27 pts are still alive. Of the 31 pts treated, 22 (71%) had high EGFR gene copy number (amplification (3) or high polysomy (19)); RR and PFS did not vary by copy number. Conclusions: 1st-line gefitinib therapy in EGFR mutation-positive NSCLC pts is feasible in a multi-institutional study, well tolerated, and yields a substantial RR and PFS. This strategy should be compared to standard chemotherapy in a genotype-directed randomized trial. No significant financial relationships to disclose.