http://www.springerprotocols.com/cdp/access/showWebFeedListing This feed provides the latest 25 protocols in the given category. http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_1 Interference with the innate apoptotic activity is a hallmark of neoplastic transformation and tumor formation. Modulation of the apoptotic cascade has been proposed as a new approach for the treatment of cancer. In this chapter, we discuss the role of apoptosis in ovarian cancer and the use of phenoxodiol as a model for the regulation of apoptosis and potential use as chemosensitizer for chemoresistant ovarian cancer cells. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_10 Apoptosis detection methodology is an ever evolving science. The caspase family of cysteine proteases plays a central role in this environmentally conserved mechanism of regulated cell death. New methods that allow for the improved detection and monitoring of the apoptosis-associated proteases are key for further advancement of our understanding of apoptosis-mediated disease states such as cancer and Alzheimer’s disease. From the use of membrane permeant fluorescent-labeled inhibitors of caspases (FLICA) probe technology, we have demonstrated their successful use as tools in the detection of apoptosis activity within the in vitro and in vivo research setting. In this chapter, we provide detailed methods for performing in vitro apoptosis detection assays in whole living cells, using flow cytometry, and 96-well fluorescence plate reader analysis methods. Furthermore, novel flow cytometry-based cytotoxicity assay methods, which incorporate the FLICA probe for early apoptosis detection, are described. Inclusion of this sensitive apoptosis detection probe component into the flow-based cytotoxicity assay format results in an extremely sensitive cytotoxicity detection mechanism. Lastly, in this chapter, we describe the use of the FLICA probe for the in vivo detection of tumor cell apoptosis in mice and rats. These early stage in vivo-type assays show great potential for whole animal apoptosis detection research. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_11 Caspase activity assays in multi-well plate formats represent powerful tools for understanding experimental modulation of the apoptotic response. These assays are configured to exploit functional, biochemical, and temporal differences in substrate specificity and selectivity, which are useful in defining the magnitude and mechanism of a compound or treatment effect. New advances in fluorescent and luminescent chemistries now enable single addition “add-mix-measure” determinations of caspase activity directly in the sample plate with unprecedented sensitivity. Unlike other more cumbersome or laborious techniques, caspase activity induction or inhibition measures are quantifiable and definitive. The highlighted techniques in this chapter are cost efficient and allow for the rapid exploration of thousands of combinations and conditions. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_12 Multiplexed assay chemistries provide for multiple measurements of cellular parameters within a single assay well. This experimental practice not only is more cost efficient but provides more informational content about a compound or treatment. For instance, multiplexed caspase activity assays can help establish the kinetics and magnitude of initiator and effector caspase induction by candidate compounds or treatments. The ability to combine the activity profiles within the same sample provides a level of normalization not possible with parallel assays. Furthermore, multiplexing caspase activity assays with viability and/or cytotoxicity assays can support conclusions regarding cytotoxic mechanism and provide normalization that may help correct for differences in cell number. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_13 Protein degradation is mediated predominantly through the ubiquitin–proteasome pathway. The importance of the proteasome in regulating degradation of proteins involved in cell-cycle control, apoptosis, and angiogenesis led to the recognition of the proteasome as a therapeutic target for cancer (1–4). The proteasome is also essential for degrading misfolded and aberrant proteins, and impaired proteasome function has been implicated in diseases such as Parkinson’s and Alzheimer’s citech13:bib05. The importance of the proteasome for general cell homeostasis has been established, and the 2004 Nobel Prize for Chemistry honored the researchers that discovered the ubiquitin–proteasome pathway. Robust, sensitive assays are essential for monitoring proteasome activity and for developing inhibitors of the proteasome. Peptide-conjugated fluorophores are widely used as substrates for monitoring proteasome activity, but fluorogenic substrates can exhibit significant background and can be problematic for screening because of cellular autoflorescence or fluorescent library compounds. To address these issues, we developed a homogeneous, bioluminescent method that combines peptide-conjugated aminoluciferin substrates and a stabilized luciferase. We have developed homogeneous, bioluminescent assays for all three proteasome activities, the chymotrypsin-like, trypsin-like, and caspase-like, using purified proteasome. We have also applied this technology to a cellular assay using the substrate for the chymotrypsin-like activity in combination with a selective membrane permeabilization step (patent pending). The proteasome assays are designed in a simple “add and read” format and have been tested in 96- and 384-well plates. The bioluminescent, coupled-enzyme format enables sensitive and rapid protease assays ideal for inhibitor screening. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_14 Here we describe a simple protocol that uses positively charged nylon membrane dot blot to profile miRNA expression. A library of 515 antisense oligodeoxynucleotides of human and mouse mature miRNAs was synthesized and spotted on GeneScreen Plus membrane using a dot-blot equipment. Total RNA or enriched small molecular weight RNAs (smwRNAs) were enzymatically radiolabeled by poly (A) polymerase and then hybridized to the nylon membrane oligo arrays. The spot signal intensity on the membrane was analyzed using phosphorimaging. This method offers a convenient and economic way to simultaneously detect the expression of hundreds of miRNAs. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_15 Caspases are central to the execution of apoptosis. Their proteolytic activity is responsible for the demise of cells in many physiological and pathological states. Great advances in understanding caspases have been made using recombinant caspase expression and enzymatic characterization. Assays to measure caspase activity in apoptotic cell extracts and the development of a reconstituted cell-free assay were also critical in establishing the hierarchy in the caspase activation cascade and comprehend how caspase-9 is activated by the apoptosome. More recently, new tools such as activity-based probes allowed us to detect caspase activation in their working environment providing readout of the system with minimal interference. This chapter describes some of the methods used by our group to study the activation mechanisms of caspases and their activity. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_16 The extrinsic apoptosis pathway is activated when certain members of the tumor necrosis factor (TNF) receptor superfamily (TNFRSF) are oligomerized by their cognate ligands that are members of the TNF superfamily (TNFSF). The apoptosis-inducing capacity of a member of the TNFRSF relies on the presence of a death domain (DD) in the intracellular portion of the receptor protein. Such receptors are also referred to as death receptors. Binding of a TNFSF ligand to a TNFRSF receptor that is expressed on the surface of a cell results in the formation of a receptor proximal protein complex. This protein complex is the platform for further signaling events within the cell. In case of death receptors like TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1/DR4), TRAIL-R2 (KILLER/APO-2/DR5/TRICK), CD95 (Fas, APO-1), or TNF receptor 1 (TNF-R1), this complex is termed death-inducing signaling complex (DISC). The compositions of the various DISCs have been intensively studied in the last 12 years. For the CD95 and the TRAIL-R1/R2 DISCs, it is now clear that the adaptor protein Fas-associated DD protein (FADD) forms part of these complexes and is necessary for recruitment of the pro-apoptotic signaling molecules caspase-8 and caspase-10. Recruitment of these proteases allows for their activation at the DISC and subsequent induction of apoptosis. The caspase-8 homologous cellular FLICE-like inhibitory protein (cFLIP) can also be recruited to the DISC. cFLIP acts as an anti-apoptotic regulator by interfering with activation of caspases 8 and 10 at the DISC. Interestingly, treatment of TRAIL-resistant tumor cells with conventional chemotherapeutic drugs or with proteasome inhibitors renders these cells sensitive for TRAIL-induced apoptosis. By applying the methodology of the biochemical analysis of the TRAIL DISC described here, we were able to show that this sensitization is mainly due to changes in the CIP[-9.5]From: Methods in Molecular Biology, vol. 414: Apoptosis and Cancer Edited by: G. Mor and A. B. Alvero © Humana Press Inc., Totowa, NJ biochemical composition of the DISC as the apoptosis-initiating protein complex of the extrinsic pathway. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_17 Gene expression analysis provides an insight into the unique and defining biomolecular characteristics of a given cell type. However, heterogeneous cellular compositions hinder gene analysis studies from most tissue samples. The laser microdissection (LMD) technique allows for the unambiguous isolation of a desired cell population. However, preserving RNA integrity can be challenging because of the deliberately limited amount of starting material, sometimes as little as a single cell. General laboratory procedures for reducing ribonuclease (RNase) activity, both in reagents and in the laboratory environment, are required for successful downstream RNA isolation and quantitation. Quality RNA can be extracted from sections made from flash-frozen and paraffin-embedded tissue. The standard histological stains such as hematoxylin and eosin (H&E), or toluidine blue, can provide visualization of the cells of interest. Following LMD, validation of RNA integrity should precede downstream analysis. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_2 A number of methods have been developed to identify the cells that undergo apoptosis by analyzing the morphological, biochemical, and molecular changes that take place during this universal biological process. The best recognized biochemical hallmark of both early and late stages of apoptosis is the activation of cysteine proteases (caspases). Detection of active caspase-3 in cells and tissues is an important method for apoptosis induced by a wide variety of apoptotic signals. Most common assays for examining caspase-3 activation include immunostaining, immunoblotting for active caspase-3, colorimetric assays using fluorochrome substrates, as well as employing the fluorescein-labeled CaspaTag pan-caspase in situ detection kit. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_3 Most authors currently quantify the frequency of apoptotic cells in a given phenotypically defined population after calculating the apoptotic index (AI), that is, the percentage of apoptotic cells displaying a specific lineage antigen (LAg) within a population of cells that remain unfragmented and retain the expression of the LAg. However, this approach has two major limitations. First, apoptotic cells fragment into apoptotic bodies that later disintegrate. Second, apoptotic cells frequently lose, partially or even completely, the cell surface expression of the LAg used for the identification of specific cell subsets. This chapter will describe a flow cytometry method to calculate the apoptotic rate (AR) that takes into account both cell fragmentation and loss of LAg expression on measurement of apoptosis using flow cytometry ratiometric cell enumeration that emerges as a more accurate method of measurement of the occurrence of apoptosis in normal and tumoral cell cultures. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_4 Tumors are heterogeneous structures that contain different cell populations. Laser capture microdissection (LCM) can be used to obtain pure cancer cells from fresh-frozen cancer tissue and the surrounded environment, thus providing an accurate snapshot of the tumor and its microenvironment in vivo. We describe a new approach to isolate pure cancer cell population and evaluate protein expression. The process includes immunocytochemistry, laser microdissection, and western blot analysis. Using this technique, we can detect proteins such as X-linked inhibitor of apoptosis protein (XIAP) and Fas ligand (FasL) with as little as 1000 cells. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_5 Apoptosis (programmed cell death) is an active process that plays a critical role in multiple biologic processes from embryologic development, to lymphocyte development and selection, and homeostasis. The two major mechanisms of cell death are referred to as the intrinsic and extrinsic pathways. These pathways lead to a cascade of events that ultimately converge to the activation of an effector enzyme, caspase-3. Caspase-3 is a cysteine protease with aspartic specificity and a well-characterized effector of apoptosis or programmed cell death signaling. The pro-form of caspase-3 (p32 caspase-3) is sequestered as a zymogen, where upon proteolysis at a conserved DEVD sequence, is converted to the active (p17 caspase-3) enzyme capable of disassembling the cell. Cell death can become disregulated under various conditions and multiple disease states (e.g., viral infection, carcinogenesis, and metastasis). Sensitive and reproducible detection of active caspase-3 is critical to advance the understanding of cellular functions and multiple pathologies of various etiologies. Here, we provide two simple and reproducible methods to measure active caspase-3 in multiple cell types and conditions using a flow cytometric-based analysis. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_6 The ChemoFx® Assay is an ex vivo assay designed to predict the sensitivity and resistance of a given patient’s solid tumor to a variety of chemotherapy agents. A portion of a patient’s solid tumor, as small as a core biopsy, is mechanically disaggregated and established in primary culture where malignant epithelial cells migrate out of tumor explants to form a monolayer. Cultures are verified as epithelial and exposed to increasing doses of selected chemotherapeutic agents. The number of live cells remaining post-treatment is enumerated microscopically using automated cell-counting software. The resultant cell counts in treated wells are compared with those in untreated control wells to generate a dose-response curve for each chemotherapeutic agent tested on a given patient specimen. Features of each dose-response curve are used to score a tumor’s response to each ex vivo treatment as “responsive,” “intermediate response,” or “non-responsive.” Collectively, these scores are used to assist an oncologist in making treatment decisions. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_7 The immediate assessment of response to therapy is most beneficial to ovarian cancer patients. This study shows the correlation of drug-induced caspase activation determined by western blot analysis and by Caspase-Glo™ assay. Our findings demonstrate that the use of the Caspase-Glo™ assay allows a simple, fast, and sensitive alternative for the evaluation of in vitro response to chemotherapy. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_8 Apoptotic markers include proteins from the intrinsic and extrinsic pathways. These cascades include both pro-apoptotic and anti-apoptotic elements. The expression levels of these elements can be assessed by immunohistochemistry (IHC) and can indicate general trends in pro- versus anti-apoptotic tendencies of the cells. IHC is particularly useful when studying large cohorts of paraffin-embedded specimens. Advances in tissue microarray (TMA) technology have facilitated evaluation of large cohorts of specimens, as cores from hundreds of patients can be represented on a single glass slide and stained in a uniform fashion. In this chapter, we discuss construction and staining methods of TMAs and present examples of assessment of apoptotic marker expression in malignant and benign cells using a novel method of automated, quantitative analysis of in situ protein expression. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-339-4_9 Since the discovery of the key role of cytochrome C in the activation of caspase 9, intense interest has focused on the role of mitochondria in apoptosis/programmed cell death. Mitochondria undergo two major alterations during apoptosis. The first is the permeabilization of the outer mitochondrial membrane. This event is tightly regulated by members of the Bcl-2 family and involves the conformational change of pro-apoptotic family members such as Bax. Second, the electrochemical gradient that is normally present across the inner mitochondrial membrane is lost (membrane depolarization). This event is sometimes mediated by the permeability transition pore (PTP). The order in which these events occur and whether one causes the other has been hotly debated in the literature. Nonetheless, the majority of reports suggest that mitochondria outer membrane permeabilization (MOMP) precedes membrane depolarization. In this chapter, methods that examine membrane depolarization and the conformational change in Bax are described. 2007-10-11T04:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1385/1-59745-017-0:1 In this chapter, methods to isolate RNA and DNA from human leukocytes for the subsequent use in molecular diagnostic tests are described. In addition, protocols for cDNA synthesis are given, both for the use in conventional reverse transcription (RT)-polymerase chain reaction (PCR), and for the use in quantitative RT-PCR reactions. Because sensitive PCR methods are commonly used in molecular diagnostics, measures to avoid contamination are described. Finally, a simple procedure to control the quality of isolated RNA is described. 2005-11-15T05:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1385/1-59745-017-0:107 With the development of fluorescence in situ hybridization (FISH), it was possible to detect the BCR-ABL fusion signal in both metaphase spreads and interphase cells of patients with chronic myeloid leukemia (CML). However, the use of FISH to detect residual disease in patients with CML post therapy was limited by the false positive rate using the early single fusion probes. Therefore, dual fusion probes that created a fusion signal on the derivative chromosome 9 in addition to the fusion sifnal on the Philadelphia chromosome or derivative chromo-some 22 were developed. Using these second-generation probes, it was discovered that a significant proportion of CML cases has a sub-microscopic deletion at the site of the ABL-BCR fusion. This chapter outlines a testing strategy to identify deleltions of the derivative chromo-some 9 and to use combinations of probes to identify residual disease in these cases. 2005-11-15T05:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1385/1-59745-017-0:115 The t(15;17) is the diagnostic hallmark of acute promyelocytic leukemia (APL). As a result, the RARA and the promyelocytic leukemia (PML) genes are fused. The use of reverse-transcription polymerase chain reaction (RT-PCR) for the detection of the PML-RARA and RARA-PML fusion genes is the only technique that defines the PML breakpoint type and that allows the definition of a correct strategy for subsequent minimal residual disease (MRD) monitoring. Standardized conditions for RT-PCR analysis of fusion transcripts from chromosome aberrations in acute leukemia, including APL, have recently been reported in the context of the Biomed-1 Concerted Action, and are described in detail in this chapter. 2005-11-15T05:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1385/1-59745-017-0:127 The last 15 yr have produced dramatic improvements in the survival rate of patients with acute promyelocytic leukemia (APL). These improvements have been due mainly to the introduction of targeted therapies and improved methods for diagnosing and monitoring this disease. The underlying molecular lesion in APL involves a t(15:17) translocation which leads to the generation of PML-RARα fusion transcripts and proteins. The PML-RARα fusion transcripts have been shown to be useful markers for establishing the diagnosis and for monitoring the response to treatment. 2005-11-15T05:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1385/1-59745-017-0:13 Chromosome analysis is an essential part of the diagnostic testing of myeloid malignancies. Good chromosome preparations are essential for a complete cytogenetic analysis. This means plentiful metaphase spreads with well-spread crisply banded chromosomes. To achieve such a result, several variables, including the growth rate of the leukemic cells, are critical. The method described in this chapter has been extensively tested and should produce reasonable results from most cases. Fluorescence in situ hybridization (FISH) is less influenced by sample variation and as a result may be obtained from either metaphase spreads or interphase cells. Moreover, FISH is capable of describing chromosome rearrangements at the gene level, rather than at the gross level shown by conventional cytogenetics. It does not, however, provide information on genetic rearrangements other than at the specific target site of the probe used, unlike conventional cytogenetics. Thus, these two techniques complement each other and are both now essential elements of chromosome analysis. 2005-11-15T05:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1385/1-59745-017-0:149 Assessing the level of residual disease in leukemia is vital for evaluating patients’ response to treatment and for identifying those at high risk of relapse. This should enable early preemptive intervention to prevent the onset of hematological relapse in those patients. One of the most common translocations in acute myeloid leukemia (AML) is the t(8;21). t(8;21) AML is characterized by a relatively good prognosis. This chapter discusses both qualitative and quantitative (real-time quantitative reverse-transcription polymerase chain reaction [RQ-PCR]) protocols for the diagnosis and minimal residual disease (MRD) monitoring in t(8;21) AML. It also discusses the importance of choosing appropriate controls for each assay. The chapter provides a simple equation for assessing the sensitivity/reliability of RQ-PCR assays, which enables scientists to assess the accuracy and reliability of their data. 2005-11-15T05:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1385/1-59745-017-0:163 During the last decade, many mutations present in myeloid leukemias have been molecularly characterized. Several of these mutations have clear prognostic impact. The molecular screening of these mutations has now become an essential part in several risk-adapted international clinical trials. Here we describe protocols for the qualitative and quantitative detection of leukemic cells that are characterized by a CBFB-MYH11 gene fusion. 2005-11-15T05:00:00Z http://www.springerprotocols.com/Abstract/doi/10.1385/1-59745-017-0:177 Idiopathic hypereosinophilic syndrome (HES) and chronic eosinophilic leukemia (CEL) are related hematological malignancies characterized by sustained, unexplained hypereosinophilia (>1,500 eosinophils/μL) (1–4). The term CEL is used when there is evidence that the disease is of clonal origin. We recently identified the FIP1L1-PDGFRA fusion gene in approx 50% of HES/CEL cases (5). Fusion of FIP1L1 to PDGFRA is the consequence of a deletion on chromosome 4, del(4)(q12q12), with the centromeric breakpoint in FIP1L1 and the telomeric breakpoint in PDGFRA. The breakpoints in FIP1L1 are diverse (introns 7 to 10), but the breakpoints in PDGFRA are always in exon 12 (encoding the juxtamembrane region). because the chromosomal deletion is only 800 kb in size, it remains undetected with standard cytogenetics. In agreement with this, most patients with HES/CEL present with a normal karyotype. Here we describe three different techniques to detect the presence of the FIP1L1-PDGFRA fusion gene in peripheral blood or bone marrow cells. 2005-11-15T05:00:00Z