Springer protocols feed by Cancer Research 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.Flow Cytometry for Non-Hodgkin and Classical Hodgkin Lymphoma
Multiparametric flow cytometry is a powerful diagnostic tool that permits rapid assessment of cellular antigen expression to quickly provide immunophenotypic information suitable for disease classification. This chapter describes a general approach for the identification of abnormal lymphoid populations by flow cytometry, including B, T, and Hodgkin lymphoma cells suitable for the clinical and research environment. Knowledge of the common patterns of antigen expression of normal lymphoid cells is critical to permit identification of abnormal populations at disease presentation and for minimal residual disease assessment. W...
Source: Springer protocols feed by Cancer Research - January 11, 2013 Category: Cancer & Oncology Source Type: news
Origin and Pathogenesis of B Cell Lymphomas
Immunoglobulin (Ig) gene remodeling by V(D)J recombination plays a central role in the generation of normal B cells, and somatic hypermutation and class switching of Ig genes are key processes during antigen-driven B cell differentiation. However, errors of these processes are involved in the development of B cell lymphomas. Ig locus-associated translocations of proto-oncogenes are a hallmark of many B cell malignancies. Additional transforming events include inactivating mutations in various tumor suppressor genes, and also latent infection of B cells with viruses, such as Epstein–Barr virus. Many B cell lymphomas r...
Source: Springer protocols feed by Cancer Research - January 11, 2013 Category: Cancer & Oncology Source Type: news
High-Throughput RNA Sequencing in B-Cell Lymphomas
High-throughput mRNA sequencing (RNA-seq) uses massively parallel sequencing to allow an unbiased analysis of both genome-wide transcription levels and mutation status of a tumor. In the RNA-seq method, complementary DNA (cDNA) is used to generate short sequence reads by immobilizing millions of amplified DNA fragments onto a solid surface and performing the sequence reaction. The resulting sequences are aligned to a reference genome or transcript database to create a comprehensive description of the analyzed transcriptome. This chapter describes a protocol to perform RNA-seq using the Illumina sequencing platform, present...
Source: Springer protocols feed by Cancer Research - January 11, 2013 Category: Cancer & Oncology Source Type: news
Molecular Methods of Virus Detection in Lymphoma
The herpesviruses Epstein-Barr virus (EBV) and human herpesvirus 8 and the retrovirus human T-cell leukemia virus type 1 are directly implicated in the pathogenesis of lymphoma and leukemia in man. EBV is associated with an expanding spectrum of lymphomas and it would appear likely that additional, possibly novel, viruses will be implicated in lymphoma pathogenesis in the future. This chapter describes techniques that may be useful in the analysis of viruses and lymphoma including a standard EBV EBER in situ hybridization assay and a degenerate PCR assay for detection of novel herpesviruses. Lastly, a method for analysis o...
Source: Springer protocols feed by Cancer Research - January 11, 2013 Category: Cancer & Oncology Source Type: news
Studying MicroRNAs in Lymphoma
MicroRNAs (miRNAs) play important roles in development, differentiation, homeostasis, and also in diseases such as lymphoma. This chapter describes methods to study the role of miRNAs in lymphoma. First, we describe a multiplex RT reaction followed by qPCR that can be used to determine differential expression of candidate miRNAs. Second, we provide a protocol for stable overexpression of miRNAs using lentiviral-based ectopic expression systems. Third, we describe a straightforward assay to determine whether the candidate miRNA may function as an oncogene or a tumor suppressor gene in lymphomagenesis. (Source: Springer prot...
Source: Springer protocols feed by Cancer Research - January 11, 2013 Category: Cancer & Oncology Source Type: news
Identification of Pathogenetically Relevant Genes in Lymphomagenesis by shRNA Library Screens
RNA interference (RNAi) is a conserved posttranscriptional gene silencing mechanism that has recently emerged as a breakthrough genetic tool in functional genomics and drug target discovery. An increasing number of studies applying RNAi in high-throughput screens have begun to unravel complex signaling networks underlying diverse cellular processes. This chapter describes an approach to construct a conditional small-hairpin (sh)RNA library and its application in human lymphoma cell lines. A library cloning procedure outlines the incorporation of shRNA sequences and random 60-mer “bar code” oligonucleotides, ena...
Source: Springer protocols feed by Cancer Research - January 11, 2013 Category: Cancer & Oncology Source Type: news
FISH and FICTION to Detect Chromosomal Aberrations in Lymphomas
Fluorescence In Situ Hybridization (FISH) is a powerful and robust technique allowing the visualization of target sequences like genes in interphase nuclei. It is widely used in routine diagnostics to identify cancer specific aberrations including lymphoma associated translocations or gene copy number changes in single tumor cells. By combining FISH with immunophenotyping—a technique called Fluorescence Immunophenotyping and Interphase Cytogenetic as a Tool for Investigation Of Neoplasia (FICTION)—it is moreover possible to identify a cell population of interest. Here we describe standard protocols for FISH and...
Source: Springer protocols feed by Cancer Research - January 11, 2013 Category: Cancer & Oncology Source Type: news
Gene Expression Profile Analysis of Lymphomas
Through the genome-wide characterization of a cell type’s transcriptome, gene expression profile analysis provides a potent tool for analyzing the pathogenesis of lymphomas and has had a major impact on the understanding of lymphoid neoplasia. The analysis of gene expression patterns of lymphomas and normal lymphocytes permits (1) the definition of molecular subtypes of lymphoma; (2) the identification of the normal cellular counterpart of a lymphoma subtype; (3) the identification of diagnostic markers and therapeutic targets; and (4) the identification of signaling pathways affected by the oncogenic transformation....
Source: Springer protocols feed by Cancer Research - January 11, 2013 Category: Cancer & Oncology Source Type: news
Enrichment of Methylated DNA by Methyl-CpG Immunoprecipitation
Normal DNA methylation is an epigenetic modification required for proper development. Aberrant DNA methylation, in contrast, is frequently observed in many different malignancies including leukemias and lymphomas. Global DNA methylation profiling addresses the methylated sequences (methylome) of patient genomes to identify disease-specific methylation patterns. Workload in methylome analyses can be considerably reduced by methylome enrichment using proteins or antibodies with high affinity to methylated DNA. Methyl-CpG Immunoprecipitation (MCIp) employs an immobilized recombinant human methyl-CpG binding domain protein 2, ...
Source: Springer protocols feed by Cancer Research - January 11, 2013 Category: Cancer & Oncology Source Type: news
MRD Detection in B-Cell Non-Hodgkin Lymphomas Using Ig Gene Rearrangements and Chromosomal Translocations as Targets for Real-Time Quantitative PCR
Minimal residual disease (MRD) diagnostics is of high clinical relevance in patients with indolent B-cell Non-Hodgkin lymphomas (B-NHL) and serves as a surrogate parameter to evaluate treatment effectiveness and long-term prognosis. MRD diagnostics performed by real-time quantitative PCR (RQ-PCR) is the gold-standard and currently the most sensitive and the most broadly applied method in follicular lymphoma (FL) and mantle cell lymphoma (MCL). RQ-PCR analysis of the junctional regions of the rearranged immunoglobulin heavy-chain gene (IgH) serves as the most broadly applicable MRD target in B-NHL (∼80%). Chromosomal tr...
Source: Springer protocols feed by Cancer Research - January 11, 2013 Category: Cancer & Oncology Source Type: news
Analysis of the Potential for Pancreatic Cancer Metastasis In Vitro and In Vivo
Pancreatic cancer remains a challenging disease, with an overall 5-year survival rate below 5%, the main reason being that it has an extremely high potential for invasion and metastasis. This potential may contribute to the fact that in more than three fourths of patients diagnosed with pancreatic cancer, it has already spread locally and to distant organs, precluding curative resection. Therefore, improved understanding of the mechanisms underlying pancreatic cancer metastasis is urgently needed. In this chapter, we describe our approaches to determining the metastatic potential of pancreatic cancer cells. Specifically, w...
Source: Springer protocols feed by Cancer Research - January 1, 2013 Category: Cancer & Oncology Source Type: news
Analysis of Transplanted Bone Marrow-Derived Cells in Chronic Pancreatitis
Pancreatic cancer is a uniformly lethal disease characterized by a strong stromal reaction called desmoplasia. Organ fibrosis is also a feature of chronic pancreatitis a known risk factor for pancreatic cancer. (Source: Springer protocols feed by Cancer Research)
Source: Springer protocols feed by Cancer Research - January 1, 2013 Category: Cancer & Oncology Source Type: news
Sphere-Forming Assays for Assessment of Benign and Malignant Pancreatic Stem Cells
Sphere-forming assays are an in vitro technique to assay both normal and neoplastic cells for clonogenic growth potential. Currently, the identification of adult progenitors in the pancreas remains an area of intense investigation. The use of sphere-forming assays provides a critical step to identify new cell types in the pancreas that are capable of clonogenic growth and differentiation. In the field of cancer biology, cancer stem cells have been defined functionally by two major criteria: their ability to undergo self-renewal and their ability to produce differentiated progeny, two conditions which satisfy the criteria o...
Source: Springer protocols feed by Cancer Research - January 1, 2013 Category: Cancer & Oncology Source Type: news
Microdissection and Culture of Murine Pancreatic Ductal Epithelial Cells
Given the complexity of morphological presentation and variability in clinical outcomes observed in epithelial cancers, it is important to understand how genomic perturbations and resultant molecular aberrations lead to acquisition of tumorigenic phenotypes. Complex 3D epithelial culture systems provide investigators with the ability to propagate and manipulate primary cells in an appropriate physical setting in order to deconstruct the contribution of a given genetic lesion(s) to the process of cellular transformation. Pancreatic ductal epithelial cells (PDEC) can give rise to pancreatic intraepithelial neoplasia&mda...
Source: Springer protocols feed by Cancer Research - January 1, 2013 Category: Cancer & Oncology Source Type: news
Quantification of Murine Pancreatic Tumors by High-Resolution Ultrasound
Ultrasonography is a powerful imaging modality that enables noninvasive, real-time visualization of abdominal organs and tissues. This technology may be adapted for use in mice through the utilization of higher frequency transducers, allowing for extremely high-resolution imaging of the mouse pancreas. This technique is particularly well suited to pancreas imaging due to the ultrasonographic properties of the normal mouse pancreas, easily accessible imaging planes for the head and tail of the mouse pancreas, and the comparative difficulty in imaging the mouse pancreas with other technologies. A suite of measurement tools i...
Source: Springer protocols feed by Cancer Research - January 1, 2013 Category: Cancer & Oncology Source Type: news
