Abstract:
:Patient-derived xenografts are a useful tool in cancer immunology, as they allow researchers to study human cancers in vivo when starting with a relatively small amount of human tumor tissue. These models make it possible to study tumor cell-intrinsic changes that occur in response to external stimuli including cytokines like interferon gamma (IFNγ) that are important for effective anti-tumor immune responses. IFNγ responsiveness can be measured by assessing surface expression of MHC class I on tumor cells, the molecule on which tumor antigens are presented to cytotoxic T cells in the tumor microenvironment. Low levels of MHC class I and lack of responsiveness have been associated with resistance to T-cell directed therapies like immune checkpoint inhibitors. In this chapter, we present a protocol for an assay to screen patient-derived xenografts for their responsiveness to IFNγ. The results of this assay can be used as a starting point for uncovering cancer cell-intrinsic mechanisms of resistance to immunotherapies in patient tumors.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Cardenas JJ,Robles-Oteiza C,Politi Kdoi
10.1016/bs.mie.2019.10.027subject
Has Abstractpub_date
2020-01-01 00:00:00pages
415-427eissn
0076-6879issn
1557-7988pii
S0076-6879(19)30440-9journal_volume
631pub_type
杂志文章abstract::Glycosaminoglycans (GAGs) are long unbranched polysaccharides, most of which are linked to a core protein to form proteoglycans. Depending on the nature of their backbone, one can discern galactosaminoglycans (chondroitin sulfate [CS] and dermatan sulfate [DS]) and glucosaminoglycans (heparan sulfate [HS], heparin, hy...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)16005-X
更新日期:2006-01-01 00:00:00
abstract::In principle, the long emission lifetimes of lanthanide chelates should enable their ultrasensitive detection in biological systems by time-resolved optical microscopy. However, most lanthanide-imaging systems cannot achieve sensitivities that exceed those of conventional fluorescence microscopes, since they are limit...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.04.030
更新日期:2020-01-01 00:00:00
abstract::Cells belonging to the monocyte/macrophage lineage are in general highly resistant to peroxynitrite. Resistance is not dependent on the scavenging of peroxynitrite itself, or of other secondary reactive species, but is rather associated with the prompt activation of a survival signaling leading to the prevention of to...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)01205-6
更新日期:2008-01-01 00:00:00
abstract::Formation of 5-methyluridine (ribothymidine) at position 54 of the T-psi loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA[uracil-54,C5]-MTases). In eukaryotes and many bacteria, the methyl donor for this reaction is generally S-adenosyl-L-methionine (S-AdoMet). However, in other bacteria, like ...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(07)25004-9
更新日期:2007-01-01 00:00:00
abstract::Cryptococcus neoformans is a yeastlike fungus that causes a lethal meningoencephalitis in a broad spectrum of immunocompromised patients and has become the most common cause of meningitis due to AIDS-related infections in Africa. Key to the development of new agents to control and prevent this infection is the identif...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)03222-9
更新日期:2008-01-01 00:00:00
abstract::A number of different analytical techniques are now available for the isolation of apoA-I, apoA-II, and apoA-IV. The choice of a particular technique is dependent on the instrumentation available, and the quantity of isolated apolipoprotein required. The isolation and characterization of the separate isoforms and the ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/0076-6879(86)28070-2
更新日期:1986-01-01 00:00:00
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)01618-2
更新日期:2008-01-01 00:00:00
abstract::Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, flu...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/bs.mie.2017.01.019
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.09.076
更新日期:2017-01-01 00:00:00
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journal_title:Methods in enzymology
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doi:10.1016/B978-0-12-386471-0.00005-5
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abstract::The three-dimensional (3D) organization of the genome is important for chromatin regulation. This organization is nonrandom and appears to be tightly correlated with or regulated by chromatin state and scaffolding proteins. To understand how specific DNA and chromatin elements contribute to the functional organization...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2015.09.028
更新日期:2016-01-01 00:00:00
abstract::Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is benefic...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/bs.mie.2016.05.025
更新日期:2016-01-01 00:00:00
abstract::Quantitative real-time polymerase chain reaction (qRT-PCR) is a flexible and scalable method for analyzing transcript abundance that can be used at a single gene or high-throughput (>100 genes) level. Information obtained from this technique can be used as an indicator of potential regulation of glycosylation at the t...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(10)79004-2
更新日期:2010-01-01 00:00:00
abstract::The anaphase-promoting complex (APC) is a central regulator of the eukaryotic cell cycle and functions as an E3 ubiquitin protein ligase to catalyze the ubiquitination of a number of cell cycle regulatory proteins. The APC contains at least 13 subunits in addition to two activator subunits, Cdc20 and Cdh1, that associ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)98017-8
更新日期:2005-01-01 00:00:00
abstract::Adenoviral vectors expressing vascular permeability factor/vascular endothelial growth factor (VPF/VEGF, VEGF-A(164)) offer a powerful method for elucidating the mechanisms of pathological angiogenesis and lymphangiogenesis and for evaluating the effectiveness of pro- and anti-angiogenesis therapies. When injected int...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)02803-6
更新日期:2008-01-01 00:00:00
abstract::As new organisms are being sequenced on a daily basis, new DNA glycosylases that recognize DNA damage can be easily identified in an effort to understand both their phylogenetics and substrate specificities. As a practical matter, existing bacterial and human homologs need to be readily available as laboratory reagent...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)08002-5
更新日期:2006-01-01 00:00:00
abstract::Complex synthetic schemes catalyzed by multienzyme systems immobilized on solid materials are gaining momentum in chemical biomanufacturing. These systems harness the high chemo-, regio-, and stereoselectivity of the enzymes and the recyclability of the heterogeneous catalysts. Moreover, when the enzymes become part o...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.12.013
更新日期:2019-01-01 00:00:00
abstract::Nitric oxide (NO) is a ubiquitous gas with potent biological effects, including vasodilation, neuronal signaling, and antimicrobial activity. NO is a free radical and can readily react with other molecules, in particular, iron centers and oxygen. At physiological concentrations in aqueous solutions, even in the presen...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)36007-8
更新日期:2008-01-01 00:00:00
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-381268-1.00016-1
更新日期:2011-01-01 00:00:00
abstract::Single-cell analysis of cellular contents by highly sensitive analytical instruments is known as chemical cytometry. A chemical cytometer typically samples one cell at a time, quantifies the cellular contents of interest, and then processes and reports that data. Automation adds the potential to perform this entire se...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/bs.mie.2019.06.016
更新日期:2019-01-01 00:00:00
abstract::Although many players of the DNA damage response and DNA repair have been identified in several systems their biochemical role is still poorly understood. The use of the Xenopus laevis egg extract cell-free system allowed biochemical dissection of DNA replication and cell cycle events in a complex biological context. ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2017.03.018
更新日期:2017-01-01 00:00:00
abstract::Rarely is any solution simply solute and water. In vivo, solutes, such as proteins and nucleic acids, swim in a sea of water, salts, ions, small molecules, and lipids, not to mention other macromolecules. In vitro, virtually all solutions contain a mixture of aqueous solvents, or "cosolvents" [i.e., solvent(s) in addi...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(07)28022-X
更新日期:2007-01-01 00:00:00
abstract::Nitration and oxidation of tyrosine, tryptophan, and methionine residues in proteins are potential markers of their interaction with peroxynitrite. This chapter describes the procedure for the detection of these nitro-oxidative modifications by tandem mass spectrometry. The peptide YGDLANWMIPGK, shown to contain a nit...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(08)01215-9
更新日期:2008-01-01 00:00:00
abstract::Life cell imaging is a tool for cell biology that has provided invaluable insights into many dynamic processes such as cell division, morphogenesis, or endo- and exocytosis. While observing cells by time-lapse imaging is a standard procedure in many systems, this technique was until recently not available for blood st...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-391856-7.00029-9
更新日期:2012-01-01 00:00:00
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/s0076-6879(03)75025-3
更新日期:2004-01-01 00:00:00
abstract::Ecological samples of fungal associations pose particular challenges for nucleic acid extraction due to the presence of several genomes. Thorough examination of the samples prior to extraction is important to assess the risks of contamination. If manual separation of symbionts or their axenic cultivation is not feasib...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)95004-0
更新日期:2005-01-01 00:00:00
abstract::Helical symmetry is commonly used for building macromolecular assemblies. Helical symmetry is naturally present in viruses and cytoskeletal filaments and also occurs during crystallization of isolated proteins, such as Ca-ATPase and the nicotinic acetyl choline receptor. Structure determination of helical assemblies b...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(10)82005-1
更新日期:2010-01-01 00:00:00
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journal_title:Methods in enzymology
pub_type: 杂志文章
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更新日期:2005-01-01 00:00:00
abstract::Carbohydrate microarrays are becoming a standard tool for glycobiologists to screen large numbers of sugars and elucidate the role of carbohydrates in biological systems. This article describes detailed methods to prepare and use microarrays containing synthetic oligosaccharides as well as a summary of the biological ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)15017-X
更新日期:2006-01-01 00:00:00
abstract::This article describes the methods and techniques used to produce mutagenized mice to conduct high-throughput forward genetic screens for circadian rhythm mutants in the mouse. In particular, we outline methods to safely prepare and administer the chemical mutagen N-nitroso-N-ethylurea (ENU) to mice. We also discuss t...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)93007-3
更新日期:2005-01-01 00:00:00