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Tang H, Wang J, Hou J, Tao Q, Huang H. O3. Proteasome inhibitor enhance histone deacetylase inhibitor mediated anti-tumor efficacy in TSCC. Oral Oncol 2011. [DOI: 10.1016/j.oraloncology.2011.06.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hashimoto S, Takazawa Y, Fushimi A, Tanabe K, Shibata Y, Ieda T, Ochiai N, Kanda H, Ohura T, Tao Q, Reichenbach SE. Global and selective detection of organohalogens in environmental samples by comprehensive two-dimensional gas chromatography–tandem mass spectrometry and high-resolution time-of-flight mass spectrometry. J Chromatogr A 2011; 1218:3799-810. [DOI: 10.1016/j.chroma.2011.04.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/19/2011] [Accepted: 04/19/2011] [Indexed: 10/18/2022]
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Low JSW, Tao Q, Ng KM, Goh HK, Shu XS, Woo WL, Ambinder RF, Srivastava G, Shamay M, Chan ATC, Popescu NC, Hsieh WS. A novel isoform of the 8p22 tumor suppressor gene DLC1 suppresses tumor growth and is frequently silenced in multiple common tumors. Oncogene 2011; 30:1923-35. [PMID: 21217778 PMCID: PMC3385516 DOI: 10.1038/onc.2010.576] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 11/15/2010] [Accepted: 11/15/2010] [Indexed: 12/18/2022]
Abstract
The critical 8p22 tumor suppressor deleted in liver cancer 1 (DLC1) is frequently inactivated by aberrant CpG methylation and/or genetic deletion and implicated in tumorigeneses of multiple tumor types. Here, we report the identification and characterization of its new isoform, DLC1 isoform 4 (DLC1-i4). This novel isoform encodes an 1125-aa (amino acid) protein with distinct N-terminus as compared with other known DLC1 isoforms. Similar to other isoforms, DLC1-i4 is expressed ubiquitously in normal tissues and immortalized normal epithelial cells, suggesting a role as a major DLC1 transcript. However, differential expression of the four DLC1 isoforms is found in tumor cell lines: Isoform 1 (longest) and 3 (short thus probably nonfunctional) share a promoter and are silenced in almost all cancer and immortalized cell lines, whereas isoform 2 and 4 utilize different promoters and are frequently downregulated. DLC1-i4 is significantly downregulated in multiple carcinoma cell lines, including 2/4 nasopharyngeal, 8/16 (50%) esophageal, 4/16 (25%) gastric, 6/9 (67%) breast, 3/4 colorectal, 4/4 cervical and 2/8(25%) lung carcinoma cell lines. The functional DLC1-i4 promoter is within a CpG island and is activated by wild-type p53. CpG methylation of the DLC1-i4 promoter is associated with its silencing in tumor cells and was detected in 38-100% of multiple primary tumors. Treatment with 5-aza-2'-deoxycytidine or genetic double knockout of DNMT1 and DNMT3B led to demethylation of the promoter and reactivation of its expression, indicating a predominantly epigenetic mechanism of silencing. Ectopic expression of DLC1-i4 in silenced tumor cells strongly inhibited their growth and colony formation. Thus, we identified a new isoform of DLC1 with tumor suppressive function. The differential expression of various DLC1 isoforms suggests interplay in modulating the complex activities of DLC1 during carcinogenesis.
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Cordero C, Liberto E, Bicchi C, Rubiolo P, Reichenbach SE, Tian X, Tao Q. Targeted and non-targeted approaches for complex natural sample profiling by GCxGC-qMS. J Chromatogr Sci 2010; 48:251-61. [PMID: 20412646 DOI: 10.1093/chromsci/48.4.251] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The present study examines the ability of targeted and non-targeted methods to provide specific and complementary information on groups of samples on the basis of their component distribution on the two-dimensional gas chromatography (GCxGC) plane. The volatile fraction of Arabica green and roasted coffee samples differing in geographical origins and roasting treatments and the volatile fraction from juniper needles, sampled by headspace-solid phase microextraction, were analyzed by GCxGC-qMS and sample profiles processed by different approaches. In the target analysis profiling, samples submitted to different roasting cycles and/or differing in origin and post-harvest treatment are characterized on the basis of known constituents (botanical, technological, and/or aromatic markers). This approach provides highly reliable results on quali-quantitative compositional differences because of the authentic standard confirmation, extending and improving the specificity of the comparative procedure to trace and minor components. On the other hand, non-targeted data-processing methods (e.g., direct image comparison and template-based fingerprinting) include in the sample comparisons and correlations all detected sample components, offering an increased discrimination potential by identifying compounds that are comparatively significant but not known targets. Results demonstrate the ability of GCxGC to explore in depth the complexity of samples and emphasize the advantages of a comprehensive and multidisciplinary approach to improve the level of information provided by GCxGC separation.
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Zheng DD, Yang JH, Tao Q, Geng M, Lin J, Yang XJ, Song JP, Li HX, Han LH, Jiang WP. Mutations in the beta-myosin heavy chain gene in southern Chinese families with hypertrophic cardiomyopathy. J Int Med Res 2010; 38:810-20. [PMID: 20819418 DOI: 10.1177/147323001003800308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In this study, 14 unrelated hypertrophic cardiomyopathy (HCM) probands were scanned by polymerase chain reaction-single-strand conformation polymorphism analysis and DNA sequencing. Three mis-sense mutations of the beta-myosin heavy chain gene, MYH7, were found: valine (Val) 606 methionine (Met), arginine (Arg) 694 leucine (Leu), and Arg 723 glycine (Gly). All are reported here for the first time in Chinese subjects. The results showed that: Val606Met is an intermediate malignancy mutation; Arg694Leu is a novel mutation with a benign phenotype; and the Arg723Gly mutation is linked to malignancy - it can lead not only to HCM but also to dilated cardiomyopathy at various ages. The clinical symptoms associated with Arg723Gly emerged early and caused more severe clinical manifestation and poorer prognosis in females than in males. Mis-sense mutations were not detected in the myosin binding protein C, cardiac, cardiac troponin T type 2, or cardiac troponin I type 3 genes. The MYH7 gene may be an HCM mutation hotspot in the Chinese and have unique features in this study population.
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Cordero C, Liberto E, Bicchi C, Rubiolo P, Schieberle P, Reichenbach SE, Tao Q. Profiling food volatiles by comprehensive two-dimensional ga schromatography coupled with mass spectrometry: Advanced fingerprinting approaches for comparative analysis of the volatile fraction of roasted hazelnuts (Corylus avellana L.) from different origins. J Chromatogr A 2010; 1217:5848-58. [DOI: 10.1016/j.chroma.2010.07.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 06/22/2010] [Accepted: 07/01/2010] [Indexed: 11/29/2022]
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Reichenbach SE, Tian X, Lindquist R, Tao Q, Henderson A, Vickerman JC. Interactive spatio-spectral analysis of three-dimensional mass-spectral (3DxMS) chemical images. SURF INTERFACE ANAL 2010. [DOI: 10.1002/sia.3553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Draheim KM, Chen HB, Tao Q, Moore N, Roche M, Lyle S. ARRDC3 suppresses breast cancer progression by negatively regulating integrin beta4. Oncogene 2010; 29:5032-47. [PMID: 20603614 PMCID: PMC2997682 DOI: 10.1038/onc.2010.250] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Large-scale genetic analyses of human tumor samples have been used to identify novel oncogenes, tumor suppressors and prognostic factors, but the functions and molecular interactions of many individual genes have not been determined. In this study we examined the cellular effects and molecular mechanism of the arrestin family member, ARRDC3, a gene preferentially lost in a subset of breast cancers. Oncomine data revealed that the expression of ARRDC3 decreases with tumor grade, metastases and recurrences. ARRDC3 overexpression represses cancer cell proliferation, migration, invasion, growth in soft agar and in vivo tumorigenicity, whereas downregulation of ARRCD3 has the opposite effects. Mechanistic studies showed that ARRDC3 functions in a novel regulatory pathway that controls the cell surface adhesion molecule, β-4 integrin (ITGβ4), a protein associated with aggressive tumor behavior. Our data indicates ARRDC3 directly binds to a phosphorylated form of ITGβ4 leading to its internalization, ubiquitination and ultimate degradation. The results identify the ARRCD3-ITGβ4 pathway as a new therapeutic target in breast cancer and show the importance of connecting genetic arrays with mechanistic studies in the search for new treatments.
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Reichenbach SE, Tian X, Tao Q, Stoll DR, Carr PW. Comprehensive feature analysis for sample classification with comprehensive two‐dimensional LC. J Sep Sci 2010; 33:1365-74. [DOI: 10.1002/jssc.200900859] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Zhang L, Zeng D, Huang H, Wang J, Tao Q, Pan C, Xu J, Zhang B, Wang A. Tissue inhibitor of metalloproteinase-2 inhibits ameloblastoma growth in a new mouse xenograft disease model. J Oral Pathol Med 2010; 39:94-102. [DOI: 10.1111/j.1600-0714.2009.00812.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Li YK, Lin X, Zhou T, Shen JQ, Tao Q, Cao GH, Xu ZA. Superconductivity induced by Ni doping in SmFe(1-x)Ni(x)AsO. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:355702. [PMID: 21828641 DOI: 10.1088/0953-8984/21/35/355702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Superconductivity with a T(c) of about 10 K is observed in the Ni-doped SmFe(1-x)Ni(x)AsO system. The measurements of resistivity and magnetic susceptibility show that the spin-density wave (SDW) order is quickly suppressed with increasing Ni content, and superconductivity emerges as x≥0.04. T(c)(mid) shows a maximum of 10.8 K at x = 0.06, and it drops to lower than 2 K as x>0.12. Meanwhile, the upper critical field (H(c2)(0)) is estimated to be about 40 T for the optimally-doped sample (x = 0.06). The normal state thermopower is negative for all the Ni-doped samples, indicating that an electron-type charge carrier dominates in the transport properties. Moreover, the magnitude of the room-temperature thermopower increases with increasing Ni content, and then shows a broad peak around x = 0.06. We found that there is an obvious correlation between the anomalously enhanced thermopower and superconductivity. A phase diagram is derived based on the transport measurements and a dome-like T(c)(x) curve is established.
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Hu XT, Zhang FB, Fan YC, Shu XS, Wong AHY, Zhou W, Shi QL, Tang HM, Fu L, Guan XY, Rha SY, Tao Q, He C. Phospholipase C delta 1 is a novel 3p22.3 tumor suppressor involved in cytoskeleton organization, with its epigenetic silencing correlated with high-stage gastric cancer. Oncogene 2009; 28:2466-75. [PMID: 19448674 DOI: 10.1038/onc.2009.92] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Located at the important tumor suppressor locus, 3p22, PLCD1 encodes an enzyme that mediates regulatory signaling of energy metabolism, calcium homeostasis and intracellular movements. We identified PLCD1 as a downregulated gene in aerodigestive carcinomas through expression profiling and epigenetic characterization. We found that PLCD1 was expressed in all normal adult tissues but low or silenced in 84% (16/19) gastric cancer cell lines, well correlated with its CpG island (CGI) methylation status. Methylation was further detected in 62% (61/98) gastric primary tumors, but none of normal gastric mucosa tissues. PLCD1 methylation was significantly correlated with tumor high stage. Detailed methylation analysis of 37 CpG sites at the PLCD1 CGI by bisulfite genomic sequencing confirmed its methylation. PLCD1 silencing could be reversed by pharmacological demethylation with 5-aza-2'-deoxycytidine, indicating a direct epigenetic silencing. Ectopic expression of PLCD1 in silenced gastric tumor cells dramatically inhibited their clonogenicity and migration, possibly through downregulating MMP7 expression and hampering the reorganization of cytoskeleton through cofilin inactivation by phosphorylation. Thus, epigenetic inactivation of PLCD1 is common and tumor-specific in gastric cancer, and PLCD1 acts as a functional tumor suppressor involved in gastric carcinogenesis.
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Reichenbach SE, Henderson A, Lindquist R, Tao Q. Efficient encoding and rapid decoding for interactive visualization of large three-dimensional hyperspectral chemical images. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:1229-1233. [PMID: 19306288 DOI: 10.1002/rcm.3962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Interactive visualization of data from a new generation of chemical imaging systems requires coding that is efficient and accessible. New technologies for secondary ion mass spectrometry (SIMS) generate large three-dimensional, hyperspectral datasets with high spatial and spectral resolution. Interactive visualization is important for chemical analysis, but the raw dataset size exceeds the memory capacities of typical current computer systems and is a significant obstacle. This paper reports the development of a lossless coding method that is memory efficient, enabling large SIMS datasets to be held in fast memory, and supports quick access for interactive visualization. The approach provides pixel indexing, as required for chemical imaging applications, and is based on the statistical characteristics of the data. The method uses differential time-of-flight to effect mass-spectral run-length-encoding and uses a scheme for variable-length, byte-unit representations for both mass-spectral time-of-flight and intensity values. Experiments demonstrate high compression rates and fast access.
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Ying J, Poon FF, Yu J, Geng H, Wong AHY, Qiu GH, Goh HK, Rha SY, Tian L, Chan ATC, Sung JJY, Tao Q. DLEC1 is a functional 3p22.3 tumour suppressor silenced by promoter CpG methylation in colon and gastric cancers. Br J Cancer 2009; 100:663-9. [PMID: 19156137 PMCID: PMC2653732 DOI: 10.1038/sj.bjc.6604888] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Promoter CpG methylation of tumour suppressor genes (TSGs) is an epigenetic biomarker for TSG identification and molecular diagnosis. We screened genome wide for novel methylated genes through methylation subtraction of a genetic demethylation model of colon cancer (double knockout of DNMT1 and DNMT3B in HCT116) and identified DLEC1 (Deleted in lung and oesophageal cancer 1), a major 3p22.3 TSG, as one of the methylated targets. We further found that DLEC1 was downregulated or silenced in most colorectal and gastric cell lines due to promoter methylation, whereas broadly expressed in normal tissues including colon and stomach, and unmethylated in expressing cell lines and immortalised normal colon epithelial cells. DLEC1 expression was reactivated through pharmacologic or genetic demethylation, indicating a DNMT1/DNMT3B-mediated methylation silencing. Aberrant methylation was further detected in primary colorectal (10 out of 34, 29%) and gastric tumours (30 out of 89, 34%), but seldom in paired normal colon (0 out of 17) and gastric (1 out of 20, 5%) samples. No correlation between DLEC1 methylation and clinical parameters of gastric cancers was found. Ectopic expression of DLEC1 in silenced HCT116 and MKN45 cells strongly inhibited their clonogenicity. Thus, DLEC1 is a functional tumour suppressor, being frequently silenced by epigenetic mechanism in gastrointestinal tumours.
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Tao Q, Scott SD, Vinodchandran NV, Osugi TT, Mueller B. Kernels for generalized multiple-instance learning. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2008; 30:2084-2098. [PMID: 18988944 DOI: 10.1109/tpami.2007.70846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The multiple-instance learning (MIL) model has been successful in numerous application areas. Recently, a generalization of this model and an algorithm for it were introduced, showing significant advantages over the conventional MIL model on certain application areas. Unfortunately, that algorithm is not scalable to high dimensions. We adapt that algorithm to one using a support vector machine with our new kernel k\wedge. This reduces the time complexity from exponential in the dimension to polynomial. Computing our new kernel is equivalent to counting the number of boxes in a discrete, bounded space that contain at least one point from each of two multisets. We show that this problem is #P-complete, but then give a fully polynomial randomized approximation scheme (FPRAS) for it. We then extend k\wedge by enriching its representation into a new kernel kmin, and also consider a normalized version of k\wedge that we call k\wedge/\vee (which may or may not not be a kernel, but whose approximation yielded positive semidefinite Gram matrices in practice). We then empirically evaluate all three measures on data from content-based image retrieval, biological sequence analysis, and the musk data sets. We found that our kernels performed well on all data sets relative to algorithms in the conventional MIL model.
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Reichenbach SE, Carr PW, Stoll DR, Tao Q. Smart templates for peak pattern matching with comprehensive two-dimensional liquid chromatography. J Chromatogr A 2008; 1216:3458-66. [PMID: 18848329 DOI: 10.1016/j.chroma.2008.09.058] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 08/29/2008] [Accepted: 09/05/2008] [Indexed: 11/26/2022]
Abstract
Comprehensive two-dimensional liquid chromatography (LCxLC) generates information-rich but complex peak patterns that require automated processing for rapid chemical identification and classification. This paper describes a powerful approach and specific methods for peak pattern matching to identify and classify constituent peaks in data from LCxLC and other multidimensional chemical separations. The approach records a prototypical pattern of peaks with retention times and associated metadata, such as chemical identities and classes, in a template. Then, the template pattern is matched to the detected peaks in subsequent data and the metadata are copied from the template to identify and classify the matched peaks. Smart Templates employ rule-based constraints (e.g., multispectral matching) to increase matching accuracy. Experimental results demonstrate Smart Templates, with the combination of retention-time pattern matching and multispectral constraints, are accurate and robust with respect to changes in peak patterns associated with variable chromatographic conditions.
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Tedoldi S, Mottok A, Ying J, Paterson JC, Cui Y, Facchetti F, van Krieken JHJM, Ponzoni M, Özkal S, Masir N, Natkunam Y, Pileri SA, Hansmann ML, Mason DY, Tao Q, Marafioti T. Selective loss of B-cell phenotype in lymphocyte predominant Hodgkin lymphoma. J Pathol 2007; 213:429-40. [DOI: 10.1002/path.2242] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Bose S, Starczynski J, Chukwuma M, Baumforth K, Wei W, Morgan S, Byrd P, Ying J, Grundy R, Mann JR, Tao Q, Taylor AMR, Murray PG, Stankovic T. Down-regulation of ATM protein in HRS cells of nodular sclerosis Hodgkin's lymphoma in children occurs in the absence ofATMgene inactivation. J Pathol 2007; 213:329-36. [PMID: 17876757 DOI: 10.1002/path.2232] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The tumour component of classical Hodgkin's lymphoma (cHL), Hodgkin Reed-Sternberg (HRS) cells, are believed to be derived from germinal centre (GC) B cells but intriguingly display a characteristic loss of B cell receptor (BCR) expression. The precise mechanisms by which BCR-negative HRS cell progenitors survive negative selection during the GC reaction remain obscure. Individuals with ataxia telangiectasia, caused by biallelic inactivation of the DNA damage response gene, ataxia telangiectasia mutated (ATM), have a higher risk of cHL development. Here we show that, in contrast to normal GC B cells that expressed low but detectable ATM protein, ATM protein was not detected in HRS cells of 17/18 cases of paediatric cHL, all but one with nodular sclerosis (NS) subtype. A comprehensive analysis of the ATM gene in microdissected HRS cells of nine representative tumours showed no evidence of either loss of heterozygosity or consistent pathogenic mutations. Furthermore, bisulphite sequencing of the ATM promoter from HRS cells of five tumours also revealed the absence of hypermethylation. Since our microarray data suggested significantly reduced ATM transcription in HRS cells compared to GC B cells, we conclude that loss of ATM expression could be the result of alterations in upstream regulators of ATM transcription. Importantly, ATM loss in paediatric cHLs has clinical implications and could be potentially exploited to guide future, less toxic, tumour-specific treatments.
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Cheng YY, Yu J, Wong YP, Man EPS, To KF, Jin VX, Li J, Tao Q, Sung JJY, Chan FKL, Leung WK. Frequent epigenetic inactivation of secreted frizzled-related protein 2 (SFRP2) by promoter methylation in human gastric cancer. Br J Cancer 2007; 97:895-901. [PMID: 17848950 PMCID: PMC2360406 DOI: 10.1038/sj.bjc.6603968] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The role of secreted frizzled-related protein (SFRP) genes in gastric cancer remains largely unknown. We determined the frequency and functional significance of SFRPs hypermethylation in human gastric cancer. The expression and methylation status of four SFRP members (SFRP1, 2, 4, and 5) in primary gastric cancer samples was screened. The biological effects of SFRP were analysed by flow cytometry, cell viability assay and in vivo tumour growth in nude mice. Among the four SFRPs, only SFRP2 was significantly downregulated in gastric cancer as compared to adjacent non-cancer samples (P<0.01). Promoter hypermethylation of SFRP2 was detected in 73.3% primary gastric cancer tissues, 37.5% of samples showing intestinal metaplasia and 20% adjacent normal gastric tissues. Bisulphite DNA sequencing confirmed the densely methylated SFRP2 promoter region. Demethylation treatment restored the expression of SFRP2 in gastric cancer cell lines. Forced expression of SFRP2 induced cell apoptosis, inhibited proliferation of gastric cancer cells and suppressed tumour growth in vivo. Moreover, methylated SFRP2 was detected in 66.7% of serum samples from cancer patients but not in normal controls. In conclusion, epigenetic inactivation of SFRP2 is a common and early event contributing to gastric carcinogenesis and may be a potential biomarker for gastric cancer.
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Law FBF, Chen YW, Wong KY, Ying J, Tao Q, Langford C, Lee PY, Law S, Cheung RWL, Chui CH, Tsao GSW, Lam KY, Wong J, Srivastava G, Tang JCO. Identification of a novel tumor transforming gene GAEC1 at 7q22 which encodes a nuclear protein and is frequently amplified and overexpressed in esophageal squamous cell carcinoma. Oncogene 2007; 26:5877-88. [PMID: 17384685 PMCID: PMC2875854 DOI: 10.1038/sj.onc.1210390] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Revised: 01/15/2007] [Accepted: 02/07/2007] [Indexed: 12/13/2022]
Abstract
By comparative DNA fingerprinting, we identified a 357-bp DNA fragment frequently amplified in esophageal squamous cell carcinomas (ESCC). This fragment overlaps with an expressed sequence tag mapped to 7q22. Further 5' and 3'-rapid amplification of cDNA ends revealed that it is part of a novel, single-exon gene with full-length mRNA of 2052 bp and encodes a nuclear protein of 109 amino acids ( approximately 15 kDa). This gene, designated as gene amplified in esophageal cancer 1 (GAEC1), was located within a 1-2 Mb amplicon at 7q22.1 identified by high-resolution 1 Mb array-comparative genomic hybridization in 6/10 ESCC cell lines. GAEC1 was ubiquitously expressed in normal tissues including esophageal and gastrointestinal organs; with amplification and overexpression in 6/10 (60%) ESCC cell lines and 34/99 (34%) primary tumors. Overexpression of GAEC1 in 3T3 mouse fibroblasts caused foci formation and colony formation in soft agar, comparable to H-ras and injection of GAEC1-transfected 3T3 cells into athymic nude mice formed undifferentiated sarcoma in vivo, indicating that GAEC1 is a transforming oncogene. Although no significant correlation was observed between GAEC1 amplification and clinicopathological parameters and prognosis, our study demonstrated that overexpressed GAEC1 has tumorigenic potential and suggest that overexpressed GAEC1 may play an important role in ESCC pathogenesis.
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Lee S, Mok T, Li H, Yim A, Wan I, Lam KC, Chan A, To KF, Tao Q. Possible correlation between SOCS1 methylation and EGFR exon 19 mutation but not exon 21 mutation in Chinese NSCLC patients. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.18113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
18113 Background: Suppressor of cytokine signaling-1 (SOCS1) and -3 (SOCS3) interact with the epidermal growth factor receptor (EGFR) to bring about the ubiquination and degradation of the receptor. Silencing of SOCS1 and SOCS3 by methylation was postulated to regulate the IL-6R/JAK-mediated STAT3 activation. Its relationship to EGFR and EGFR mutations in lung cancer remains unclear. Here, we examined the relationship between EGFR mutations and methylation of SOCS1 and SOCS3 in Chinese NSCLC patients. Methods: EGFR mutations were assessed in DNAs from microdissected tumor cells. PCR products were purified and sequenced using the BigDye Terminator Cycle Sequencing Kit (Applied Biosystem) and the ABI 3100 Genetic Analyzer. For methylation analyses of SOCS1 and SOCS3, DNAs were extracted from paraffin sections of tumor tissues, bisulfite treated and analyzed by methylation- specific PCR (MSP). Results: Data is available from 9 lung cancer cell lines and 20 tumor samples. Five EGFR-wild type cell lines had methylation for SOCS1. We found EGFR exon 19 mutation in 5 (25%) tumors, exon 21 mutation (L858R) in 2 (10%) tumors, and 1 (5%) tumor had double mutations. Four of 5 (80%) tumors with exon 19 mutation and none (0%) of the tumors with exon 21 mutation had SOCS1 methylation, comparing to only 2 of 12 (17%) EGFR-wild type tumors had SOCS1 methylation. SOCS3 methylation was not detected in any of the primary tumors or cell lines. Conclusions: Our preliminary findings suggest that SOCS1 methylation might be positively correlated with EGFR exon 19 mutation but exclusive from exon 21 mutation. A following study with larger sample size is currently under way. SOCS1 methylation may explain the better tumor response associated with EGFR exon 19 mutation. No significant financial relationships to disclose.
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Soo R, Wu J, Aggarwal A, Tao Q, Hsieh W, Putti T, Tan K, Soon W, Lai Y, Mow B, Hsu S, Loh K, Tan L, Tan P, Goh BC. Correction to: Celecoxib reduces microvessel density in patients treated with nasopharyngeal carcinoma and induces changes in gene expression. Ann Oncol 2006; 17: 1625–1630. Ann Oncol 2007. [DOI: 10.1093/annonc/mdm054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Soo RA, Wu J, Aggarwal A, Tao Q, Hsieh W, Putti T, Tan KB, Low JSW, Soon WL, Lai YF, Mow B, Hsu S, Loh KS, Tan L, Tan P, Goh BC. Celecoxib reduces microvessel density in patients treated with nasopharyngeal carcinoma and induces changes in gene expression. Ann Oncol 2006; 17:1625-30. [PMID: 17008411 DOI: 10.1093/annonc/mdl283] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Celecoxib is a selective cyclooxygenase-2 inhibitor with antitumor and antiangiogenic activity. We sought to determine pharmacodynamic change in tumors of patients with nasopharyngeal carcinoma (NPC) treated with celecoxib. METHODS Tumor biopsies were obtained before and after treatment with celecoxib 400 mg b.i.d. for 14 days in patients with newly diagnosed, untreated NPC. Tumor angiogenesis and cell proliferation were assessed by immunohistochemistry and gene expression by microarray analysis. Plasma celecoxib concentrations were obtained on days 8 and 14. RESULTS Paired samples were analyzed in 15 patients. Microvessel density was reduced in post-treatment samples and mean celecoxib levels reached therapeutic levels. Thirty-five genes (27 down-regulated, eight up-regulated) were differentially expressed on microarray analysis (p < 0.001). Down-regulated genes included cell cycle regulation-related (cyclin-dependent kinase 2, YES1), transcription factor (TRIP-Br2), whereas the antigen processing and presentation-related gene HLA-DM B was up-regulated. CONCLUSION Celecoxib reduced angiogenesis and induced tumor transcriptional changes. Further characterization of these transcriptional changes in vivo is needed to provide further insights into the effects of celecoxib in neoplastic tissue. Our findings provide a rationale for clinical studies aimed at assessing the efficacy of celecoxib in the treatment of NPC.
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Seng TJ, Low JSW, Li H, Cui Y, Goh HK, Wong MLY, Srivastava G, Sidransky D, Califano J, Steenbergen RDM, Rha SY, Tan J, Hsieh WS, Ambinder RF, Lin X, Chan ATC, Tao Q. The major 8p22 tumor suppressor DLC1 is frequently silenced by methylation in both endemic and sporadic nasopharyngeal, esophageal, and cervical carcinomas, and inhibits tumor cell colony formation. Oncogene 2006; 26:934-44. [PMID: 16862168 DOI: 10.1038/sj.onc.1209839] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Identification of tumor suppressor genes (TSG) silenced by methylation uncovers mechanisms of tumorigenesis and identifies new epigenetic tumor markers for early cancer detection. Both nasopharyngeal carcinoma (NPC) and esophageal carcinoma are major tumors in Southern China and Southeast Asia. Through expression subtraction of NPC, we identified Deleted in Liver Cancer 1 (DLC1)/ARHGAP7 (NM_006094)--an 8p22 TSG as a major downregulated gene. Although expressed in all normal tissues, DLC1 was silenced or downregulated in 11/12 (91%) NPC, 6/15 (40%) esophageal, 5/8 (63%) cervical and 3/9 (33%) breast carcinoma cell lines. No genetic deletion of DLC1 was detected in NPC although a hemizygous deletion at 8p22-11 was found by 1-Mb array-CGH in some cell lines. We then located the functional DLC1 promoter by 5'-RACE and promoter activity assays. This promoter was frequently methylated in all downregulated cell lines and in a large collection of primary tumors including 89% (64/72) NPC (endemic and sporadic types), 51% (48/94) esophageal, 87% (7/8) cervical and 36% (5/14) breast carcinomas, but seldom in paired surgical marginal tissues and not in any normal epithelial tissue. The transcriptional silencing of DLC1 could be reversed by 5-aza-2'-deoxycytidine or genetic double knock-out of DNMT1 and DNMT3B. Furthermore, ectopic expression of DLC1 in NPC and esophageal carcinoma cells strongly inhibited their colony formation. We thus found frequent epigenetic silencing of DLC1 in NPC, esophageal and cervical carcinomas, and a high correlation of methylation with its downregulation, suggesting a predominant role of epigenetic inactivation. DLC1 appears to be a major TSG implicated in the pathogenesis of these tumors, and should be further tested as a molecular biomarker in patients with these cancers.
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Ying J, Li H, Cui Y, Wong AHY, Langford C, Tao Q. Epigenetic disruption of two proapoptotic genes MAPK10/JNK3 and PTPN13/FAP-1 in multiple lymphomas and carcinomas through hypermethylation of a common bidirectional promoter. Leukemia 2006; 20:1173-5. [PMID: 16572203 DOI: 10.1038/sj.leu.2404193] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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