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Khoo B.L.,National University of Singapore | Warkiani M.E.,Singapore Alliance for Research and Technology Center | Guan G.,Singapore Alliance for Research and Technology Center | Guan G.,National University of Singapore | And 12 more authors.
IFMBE Proceedings | Year: 2014

Detection, enumeration and characterization of rare circulating tumor cells (CTCs) from the peripheral blood of cancer patients potentially provide critical insights into tumor biology and is promising for cancer diagnosis and prognosis. Here, we present a novel multiplexed spiral microfluidic device for ultra-high throughput, label-free enrichment of CTCs from clinically relevant blood volumes. The fast processing time of the technique (7.5 mL blood in < 5 min) and high sensitivity of the device lends itself to a broad range of potential genomic and transcriptomic applications. The method can specifically separate and preserve all fractions of blood (i.e., plasma, CTCs and PBMC) for diverse downstream analysis. CTCs were detected from 100% (10/10) of blood samples collected from patients with advanced stage metastatic breast (12- 56 CTC/ml) or lung cancer (30-153 CTC/ml). Cancer cells were characterized with immunostaining and fluorescence in situ hybridization (FISH) (HER2/neu). Retrieved cells were unlabelled and hence more viable for propagation and other informative analysis such as the next generation sequencing (NGS) to guide treatment and individualized patient care. © Springer International Publishing Switzerland 2014. Source


Tan D.S.W.,National Cancer Center | Tan D.S.W.,Cancer Therapeutics Research Laboratory | Tan D.S.W.,Genome Institute of Singapore | Camilleri-Broet S.,University of Paris Descartes | And 14 more authors.
International Journal of Cancer | Year: 2014

Non-small-cell lung cancer (NSCLC) is a heterogeneous disease, with a burden of genomic alterations exceeding most other tumors. The goal of our study was to evaluate the frequencies of co-occurring mutations and copy-number aberrations (CNAs) within the same tumor and to evaluate their potential clinical impact. Mass-spectrometry based mutation profiling using a customized lung cancer panel evaluating 214 mutations across 26 key NSCLC genes was performed on 230 nonsquamous NSCLC and integrated with genome-wide CNAs and clinical variables. Among the 138 cases having at least one mutation, one-third (41, 29.7%) showed two or more mutations, either in the same gene (double mutation) or in different genes (co-mutations). In epidermal growth factor receptor (EGFR) mutant cancers, there was a double mutation in 18% and co-mutations in the following genes: TP53 (10%), PIK3CA (8%), STK11 (6%) and MET (4%). Significant relationships were detected between EGFR mutation and 1p, 7p copy gains (harboring the EGFR gene) as well as 13q copy loss. KRAS mutation was significantly related with 1q gain and 3q loss. For Stage I, tumors harboring at least one mutation or PIK3CA mutation were significantly correlated with poor prognosis (p-value = 0.02). When combining CNAs and mutational status, patients having both KRAS mutation and the highest related CNA (3q22.3 copy loss) showed a significant poorer prognosis (p-value = 0.03). Our study highlights the clinical relevance of studying tumor complexity by integrative genomic analysis and the need for developing assays that broadly screen for both "actionable" mutations and copy-number alterations to improve precision of stratified treatment approaches. What's New? Personalized therapy in non-small cell lung cancer (NSCLC) is underpinned by the fact that tumor cell growth and survival depends on single gene alterations, that have become prime candidates for targeted therapeutics. Here, high-sensitivity multiplexed mutation profiling and integration of whole genome SNP array analysis were used to examine mutational status and molecular heterogeneity in NSCLC. The findings show high frequencies of co-existing mutations and copy-number aberrations within the same tumor. This complex pattern potentially influences clinical outcomes and highlights the challenges in targeting a single-driver event. The results further indicate that future tumor profiling should account for molecular heterogeneity. © 2014 UICC. Source


Khoo B.L.,National University of Singapore | Warkiani M.E.,Singapore Alliance for Research and Technology Center | Tan D.S.-W.,National Cancer Center Singapore | Tan D.S.-W.,Cancer Therapeutics Research Laboratory | And 17 more authors.
PLoS ONE | Year: 2014

Background: Circulating tumor cells (CTCs) are cancer cells that can be isolated via liquid biopsy from blood and can be phenotypically and genetically characterized to provide critical information for guiding cancer treatment. Current analysis of CTCs is hindered by the throughput, selectivity and specificity of devices or assays used in CTC detection and isolation. Methodology/Principal Findings: Here, we enriched and characterized putative CTCs from blood samples of patients with both advanced stage metastatic breast and lung cancers using a novel multiplexed spiral microfluidic chip. This system detected putative CTCs under high sensitivity (100%, n = 56) (Breast cancer samples: 12-1275 CTCs/ml; Lung cancer samples: 10-1535 CTCs/ml) rapidly from clinically relevant blood volumes (7.5 ml under 5 min). Blood samples were completely separated into plasma, CTCs and PBMCs components and each fraction were characterized with immunophenotyping (Pan-cytokeratin/CD45, CD44/CD24, EpCAM), fluorescence in-situ hybridization (FISH) (EML4-ALK) or targeted somatic mutation analysis. We used an ultra-sensitive mass spectrometry based system to highlight the presence of an EGFR-activating mutation in both isolated CTCs and plasma cell-free DNA (cf-DNA), and demonstrate concordance with the original tumor-biopsy samples. Conclusions/Significance: We have clinically validated our multiplexed microfluidic chip for the ultra high-throughput, lowcost and label-free enrichment of CTCs. Retrieved cells were unlabeled and viable, enabling potential propagation and realtime downstream analysis using next generation sequencing (NGS) or proteomic analysis. Source


Leong H.S.,Cancer Therapeutics Research Laboratory | Chong F.T.,Cancer Therapeutics Research Laboratory | Sew P.H.,Cancer Therapeutics Research Laboratory | Lau D.P.,Cancer Therapeutics Research Laboratory | And 6 more authors.
Stem Cells Translational Medicine | Year: 2014

Emerging data suggest that cancer stem cells (CSCs) exist in equilibrium with differentiated cells and that stochastic transitions between these states can account for tumor heterogeneity and drug resistance. The aim of this study was to establish an in vitro system that recapitulates stem cell plasticity in head and neck squamous cell cancers (HNSCCs) and identify the factors that play a role in the maintenance and repopulation of CSCs. Tumor spheres were established using patient-derived cell lines via anchorage-independent cell culture techniques. These tumor spheres were found to have higher aldehyde dehydrogenase (ALD) cell fractions and increased expression of Kruppel-like factor 4, SRY (sex determining region Y)-box 2, and Nanog and were resistant to γ-radiation, 5-fluorouracil, cisplatin, and etoposide treatment compared with monolayer culture cells. Monolayer cultures were subject to single cell cloning to generate clones with high and low ALD fractions. ALDHigh clones showed higher expression of stem cell and epithelial-mesenchymal transition markers compared with ALDLow clones. ALD fractions, representing stem cell fractions, fluctuated with serial passaging, equilibrating at a level specific to each cell line, and could be augmented by the addition of epidermal growth factor (EGF) and/or insulin. ALDHigh clones showed increased EGF receptor (EGFR) and insulin-like growth factor-1 receptor (IGF-1R) phosphorylation, with increased activation of downstream pathways compared with ALDLow clones. Importantly, blocking these pathways using specific inhibitors against EGFR and IGF-1R reduced stem cell fractions drastically. Taken together, these results show that HNSCC CSCs exhibit plasticity, with the maintenance of the stem cell fraction dependent on the EGFR and IGF-1R pathways and potentially amenable to targeted therapeutics. © AlphaMed Press 2014. Source


Tan D.S.W.,Cancer Therapeutics Research Laboratory | Tan D.S.W.,National Cancer Center | Wang W.,The Surgical Center | Leong H.S.,Cancer Therapeutics Research Laboratory | And 7 more authors.
BMC Cancer | Year: 2014

Background: Oral tongue squamous cell carcinomas (TSCC) are a unique subset of head and neck cancers with a distinct demographic profile, where up to half of the cases are never smokers. A small proportion of patients with OSCC are known to respond to EGFR TKI. We used a high-sensitivity mass spectrometry-based mutation profiling platform to determine the EGFR mutation status, as well as other actionable alterations in a series of Asian TSCC.Methods: 66 TSCC patients treated between 1998-2009 with complete clinico-pathologic data were included in this study. Somatic mutation profiling was performed using Sequenom LungCarta v1.0, and correlated with clinical parameters.Results: Mutations were identified in 20/66(30.3%) of samples and involved TP53, STK11, MET, PIK3CA, BRAF and NRF2. No activating EGFR mutations or KRAS mutations were discovered in our series, where just over a third were never smokers. The most common mutations were in p53 (10.6%; n = 7) and MET (10.6%, n = 11) followed by STK11 (9.1%, n = 6) and PIK3CA (4.5%, n = 3). BRAF and NRF2 mutations, which are novel in TSCC, were demonstrated in one sample each. There was no significant correlation between overall mutation status and smoking history (p = 0.967) or age (p = 0.360). Positive MET alteration was associated with poorer loco-regional recurrence free survival (LRFS) of 11 months [vs 90 months in MET-negative group (p = 0.008)]. None of the other mutations were significantly correlated with LRFS or overall survival. Four of these tumors were propagated as immortalized cell lines and demonstrated the same mutations as the original tumor.Conclusions: Using the Sequenom multiplexed LungCarta panel, we identified mutations in 6 genes, TP53, STK11, MET, PIK3CA, BRAF and NRF2, with the notable absence of EGFR and HER2 mutations in our series of Asian OSCC. Primary cell line models recapitulated the mutation profiles of the original primary tumours and provide an invaluable resource for experimental cancer therapeutics. © 2014 Tan et al.; licensee BioMed Central Ltd. Source

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