Abstract:
:We developed a novel approach for conducting multisample, multigene, ultradeep bisulfite sequencing analysis of DNA methylation patterns in clinical samples. A massively parallel sequencing-by-synthesis method (454 sequencing) was used to directly sequence >100 bisulfite PCR products in a single sequencing run without subcloning. We showed the utility, robustness, and superiority of this approach by analyzing methylation in 25 gene-related CpG rich regions from >40 cases of primary cells, including normal peripheral blood lymphocytes, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), follicular lymphoma (FL), and mantle cell lymphoma (MCL). A total of 294,631 sequences was generated with an average read length of 131 bp. On average, >1,600 individual sequences were generated for each PCR amplicon far beyond the few clones (<20) typically analyzed by traditional bisulfite sequencing. Comprehensive analysis of CpG methylation patterns at a single DNA molecule level using clustering algorithms revealed differential methylation patterns between diseases. A significant increase in methylation was detected in ALL and FL samples compared with CLL and MCL. Furthermore, a progressive spreading of methylation was detected from the periphery toward the center of select CpG islands in the ALL and FL samples. The ultradeep sequencing also allowed simultaneous analysis of genetic and epigenetic data and revealed an association between a single nucleotide polymorphism and the methylation present in the LRP1B promoter. This new generation of methylome sequencing will provide digital profiles of aberrant DNA methylation for individual human cancers and offers a robust method for the epigenetic classification of tumor subtypes.
journal_name
Cancer Resjournal_title
Cancer researchauthors
Taylor KH,Kramer RS,Davis JW,Guo J,Duff DJ,Xu D,Caldwell CW,Shi Hdoi
10.1158/0008-5472.CAN-07-1016subject
Has Abstractpub_date
2007-09-15 00:00:00pages
8511-8issue
18eissn
0008-5472issn
1538-7445pii
67/18/8511journal_volume
67pub_type
杂志文章相关文献
CANCER RESEARCH文献大全abstract::To improve tumor:tissue ratios in immunoscintigraphy, a three-step targeting method has been developed. The reagents used were (a) a radioactive, low molecular weight chelate prepared from ionic gallium and a phenolic polyaminocarboxylic acid, which can be labeled either with the single-photon emitter 67Ga or with the...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1995-01-01 00:00:00
abstract::The murine monoclonal antibodies TURP-27 and HNK-1 have been shown to detect antigens which are heavily expressed by benign prostatic hyperplasia and carcinoma of the prostate. Western blot analysis of prostate extracts showed that monoclonal antibodies TURP-27 and HNK-1 bound glycoproteins with molecular weights of 1...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1991-05-01 00:00:00
abstract::To elucidate the role of cyclin E in cell growth and tumorigenesis in mammary epithelial cells, we have used retrovirus-mediated transduction to generate derivatives of the nontransformed HC11 mouse mammary epithelial cell line that stably express a human cyclin E cDNA (HU4). These derivatives expressed two distinct f...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1996-03-15 00:00:00
abstract::Cancer vaccine feasibility would benefit from reducing the number and duration of vaccinations without diminishing efficacy. However, the duration of in vivo studies and the huge number of possible variations in vaccination protocols have discouraged their optimization. In this study, we employed an established mouse ...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-10-0701
更新日期:2010-10-15 00:00:00
abstract::Alterations in mitochondrial DNA (mtDNA) were once thought to be predominantly innocuous to cell growth. Recent evidence suggests that mtDNA undergo naturally occurring alterations, including mutations and polymorphisms, which profoundly affect the cells in which they appear and contribute to a variety of diseases, in...
journal_title:Cancer research
pub_type: 杂志文章,评审
doi:10.1158/0008-5472.CAN-17-1939
更新日期:2017-11-15 00:00:00
abstract::A model for cell detachment which may influence metastasis in vivo is described involving the transfer of hamster melanoma cells from aggregates of those tumor cells to hamster fibroblast aggregates. The aggregates were made by the spontaneous association of cultured cells. Tumor and fibroblast aggregates were then in...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1979-06-01 00:00:00
abstract::We developed a fully automated three-dimensional cell tracking system that quantified the effect of extracellular matrix components on the infiltration and migration of tumor cells. The three-dimensional trajectories of two highly invasive cell lines, the human HT-1080 fibrosarcoma and the human MDA-MB-231 adenocarcin...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:2002-09-15 00:00:00
abstract::A major goal of cancer research is to match specific therapies to molecular targets in cancer. Genome-scale expression profiling has identified new subtypes of cancer based on consistent patterns of variation in gene expression, leading to improved prognostic predictions. However, how these new genetic subtypes of can...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-07-0382
更新日期:2008-01-15 00:00:00
abstract::The inactivation of the tumor suppressor gene p53 has been demonstrated in a variety of human tumors. In this study, we present a p53 gene analysis of 13 uterine carcinoma cell lines. Sequencing analysis of the entire coding region revealed mutations changing the p53 amino acid composition in all six endometrial carci...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1991-12-15 00:00:00
abstract::Members of the INK4 family of cyclin-dependent kinase (CDK) inhibitors specifically bind and inhibit the G1-specific CDK molecules CDK4 and CDK6. One of the INK4 molecules, p16, is also known as multiple tumor suppressor and has been found to be mutated or deleted in various tumors and cell lines. We have previously i...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1999-02-01 00:00:00
abstract::Arzoxifene ([6-hydroxy-3-[4-[2-(1-piperidinyl)-ethoxy]phenoxy]-2-(4-methoxyphenyl)]benzo[b]thiophene) is a selective estrogen receptor modulator (SERM) that is a potent estrogen antagonist in mammary and uterine tissue while acting as an estrogen agonist to maintain bone density and lower serum cholesterol. Arzoxifene...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:2001-12-01 00:00:00
abstract::Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) is an important member of the TNF superfamily with great potential in cancer therapy. Luteolin is a dietary flavonoid commonly found in some medicinal plants. Here we found that pretreatment with a noncytotoxic concentration of luteolin significantl...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-04-3875
更新日期:2005-09-01 00:00:00
abstract::Inflammasomes are key regulators of innate immunity in chronic inflammatory disorders and autoimmune diseases, but their role in inflammation-associated tumorigenesis remains ill-defined. Here we reveal a protumorigenic role in gastric cancer for the key inflammasome adaptor apoptosis-related speck-like protein contai...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-17-1887
更新日期:2018-03-01 00:00:00
abstract::Serial pulmonary function tests including single-breath carbon monoxide-diffusing capacity (DLCO), forced vital capacity (FVC), and forced expiratory volume in 1 sec were performed in a relatively homogeneous group of male patients with germ cell tumors treated with vinblastine, bleomycin, and cis-diamminedichloroplat...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1979-12-01 00:00:00
abstract::Whole-slide histology images contain information that is valuable for clinical and basic science investigations of cancer, but extracting quantitative measurements from these images is challenging for researchers who are not image analysis specialists. In this paper, we describe HistomicsML2, a software tool for learn...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-20-0668
更新日期:2020-12-21 00:00:00
abstract::SMYD3 methyltransferase is nearly undetectable in normal human tissues but highly expressed in several cancers, including breast cancer, although its contributions to pathogenesis in this setting are unclear. Here we report that histone H2A.Z.1 is a substrate of SMYD3 that supports malignancy. SMYD3-mediated dimethyla...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-16-0500
更新日期:2016-10-15 00:00:00
abstract::Tumors are complex tissues composed of transformed epithelial cells as well as cancer-activated fibroblasts (CAF) that facilitate epithelial tumor cell invasion. We show here that CAFs and other mesenchymal cells rely much more on glutamine than epithelial tumor cells; consequently, they are more sensitive to inhibiti...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-20-0622
更新日期:2021-01-15 00:00:00
abstract::The process of monoclonal antibody (MAb) binding to tumor cells is greatly influenced by the biology of the respective antigen. This was concluded from an analysis of binding and release of MAbs and MAb fragments to melanoma cells at different concentration levels and different temperatures. With an antigen known to b...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1986-08-01 00:00:00
abstract::Between February 1987 and July 1988, 45 patients with advanced refractory cancer were treated with LY186641, a diarylsulfonylurea that has shown a broad spectrum of activity in preclinical testing. Patients received a weekly p.o. dose of LY186641 for 6 consecutive weeks; responding and stable patients continued weekly...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1989-09-15 00:00:00
abstract::A low molecular weight cytoplasmic protein (Mr 19,000-22,000) has been reported to be overexpressed in some multidrug-resistant cells. We have found that a cytoplasmic protein with a molecular weight of 22,000 is highly expressed in the human myelogenous leukemia K562 cells resistant to Adriamycin (K562/ADM). The Mr 2...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1988-06-01 00:00:00
abstract::Epidemiologic studies have reported the underrepresentation of cervical precancerous lesions caused by human papillomavirus (HPV) types 18 and 45 (HPV18/45) compared with the proportion of cervical cancers attributed to these HPV types. We investigated the timing of diagnosis of histologic cervical intraepithelial neo...
journal_title:Cancer research
pub_type: 杂志文章,随机对照试验
doi:10.1158/0008-5472.CAN-08-4192
更新日期:2009-04-15 00:00:00
abstract::The accumulated literature suggests that altering the immune capacities of animals or humans seldom has detectable effects on tumor incidence nor, it seems, does the growth of an untransplanted tumor, either spontaneous or induced, immunize the host against the growth of a subsequent implant of that tumor. These obser...
journal_title:Cancer research
pub_type: 杂志文章,评审
doi:
更新日期:1994-02-15 00:00:00
abstract::Deoxycytidine kinase (DCK) is a key enzyme for the activation of a broad spectrum of nucleoside-based chemotherapy drugs (e.g., gemcitabine); low DCK activity is one of the most important causes of cancer drug-resistance. Noninvasive imaging methods that can quantify DCK activity are invaluable for assessing tumor res...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-18-3565
更新日期:2019-05-15 00:00:00
abstract::A number of metabolic inhibitors and chemotherapeutic agents have been found to increase the sensitivity of a chemically induced guinea pig hepatoma (line 1) to killing by antibody and complement. We have investigated whether the mechanism whereby these drugs increase sensitivity to killing is attributable to their pr...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1977-05-01 00:00:00
abstract::The vascular endothelial growth factor (VEGF) plays a key role in tumor angiogenesis. However, clinical trials targeting the VEGF pathway are often ineffective, suggesting that other factors/pathways are also important in tumor angiogenesis. We have previously shown that the Notch ligand Delta-like 4 (DLL4) is up-regu...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-07-0969
更新日期:2007-12-01 00:00:00
abstract::Culture of human peripheral blood leukocytes with interleukin 2 (IL-2) stimulates their differentiation into lymphokine-activated killer (LAK) cells, with a broad range of cytotoxicity against fresh tumor cells and tumor cell lines (Grimm et al., J. Exp. Med., 155: 1823-1841, 1982). We chose to utilize a molecular app...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1989-02-15 00:00:00
abstract::Studies involving transcriptomics have revealed multiple molecular subtypes of hepatocellular carcinoma (HCC). Positron emission tomography/computed tomography (PET/CT) has also identified distinct molecular imaging subtypes, including those with increased and decreased choline metabolism as measured by the tissue upt...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-18-3837
更新日期:2019-04-01 00:00:00
abstract::We constructed a genome-wide transcriptome map of non-small cell lung carcinomas based on gene-expression profiles generated by serial analysis of gene expression (SAGE) using primary tumors and bronchial epithelial cells of the lung. Using the human genome working draft and the public databases, 25,135 nonredundant U...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:2002-06-15 00:00:00
abstract::An assay has been developed and measurements of aryl hydrocarbon [benzo(a)pyrene] hydroxylase have been made in peripheral blood monocytes from a human population. Treatment with benz(a)anthracene in cell culture increased aryl hydrocarbon hydroxylase activity from 6.5 to 37-fold in monocytes from each of 25 apparentl...
journal_title:Cancer research
pub_type: 杂志文章
doi:
更新日期:1976-06-01 00:00:00
abstract::There is little information on early molecular events in the development of N-nitrosomethylbenzylamine (NMBA)-induced rat esophageal tumorigenesis and of the effects of chemopreventive agents on these events. In this study, we identified genes in rat esophagus that were differentially expressed in response to short-te...
journal_title:Cancer research
pub_type: 杂志文章
doi:10.1158/0008-5472.CAN-06-4531
更新日期:2007-07-01 00:00:00