Design of a functional cyclic HSV1-TK reporter and its application to PET imaging of apoptosis.

Abstract:

:Positron emission tomography (PET) is a sensitive and noninvasive imaging method that is widely used to explore molecular events in living subjects. PET can precisely and quantitatively evaluate cellular apoptosis, which has a crucial role in various physiological and pathological processes. In this protocol, we describe the design and use of an engineered cyclic herpes simplex virus 1-thymidine kinase (HSV1-TK) PET reporter whose kinase activity is specifically switched on by apoptosis. The expression of cyclic TK (cTK) in healthy cells leads to inactive product, whereas the activation of apoptosis through the caspase-3 pathway cleaves cTK, thus restoring its activity and enabling PET imaging. In addition to detailing the design and construction of the cTK plasmid in this protocol, we include assays for evaluating the function and specificity of the cTK reporter in apoptotic cells, such as assays for measuring the cell uptake of PET tracer in apoptotic cells, correlating doxorubicin (Dox)-induced cell apoptosis to cTK function recovery, and in vivo PET imaging of cancer cell apoptosis, and we also include corresponding data acquisition methods. The time to build the entire cTK reporter is ∼2-3 weeks. The selection of a stable cancer cell line takes ∼4-6 weeks. The time to implement assays regarding cTK function in apoptotic cells and the in vivo imaging varies depending on the experiment. The cyclization strategy described in this protocol can also be adapted to create other reporter systems for broad biomedical applications.

journal_name

Nat Protoc

journal_title

Nature protocols

authors

Wang Z,Wang F,Hida N,Kiesewetter DO,Tian J,Niu G,Chen X

doi

10.1038/nprot.2015.048

subject

Has Abstract

pub_date

2015-05-01 00:00:00

pages

807-21

issue

5

eissn

1754-2189

issn

1750-2799

pii

nprot.2015.048

journal_volume

10

pub_type

杂志文章
  • MicroRNA detection by northern blotting using locked nucleic acid probes.

    abstract::MicroRNAs (miRNAs) are short, about 21 nucleotides in length, noncoding, regulatory RNA molecules representing a new layer in post-transcriptional regulation of gene expression. Intensive miRNA research has necessitated the development of effective miRNA detection methods such as northern analyses, quantitative real-t...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.528

    authors: Várallyay E,Burgyán J,Havelda Z

    更新日期:2008-01-01 00:00:00

  • Efficient delivery of nuclease proteins for genome editing in human stem cells and primary cells.

    abstract::Targeted nucleases, including zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9), have provided researchers with the ability to manipulate nearly any genomic sequence in hu...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.117

    authors: Liu J,Gaj T,Yang Y,Wang N,Shui S,Kim S,Kanchiswamy CN,Kim JS,Barbas CF 3rd

    更新日期:2015-11-01 00:00:00

  • Derivation of snake venom gland organoids for in vitro venom production.

    abstract::More than 400,000 people each year suffer adverse effects following bites from venomous snakes. However, snake venom is also a rich source of bioactive molecules with known or potential therapeutic applications. Manually 'milking' snakes is the most common method to obtain venom. Safer alternative methods to produce v...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-020-00463-4

    authors: Puschhof J,Post Y,Beumer J,Kerkkamp HM,Bittenbinder M,Vonk FJ,Casewell NR,Richardson MK,Clevers H

    更新日期:2021-01-27 00:00:00

  • Using Raman spectroscopy to characterize biological materials.

    abstract::Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and p...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2016.036

    authors: Butler HJ,Ashton L,Bird B,Cinque G,Curtis K,Dorney J,Esmonde-White K,Fullwood NJ,Gardner B,Martin-Hirsch PL,Walsh MJ,McAinsh MR,Stone N,Martin FL

    更新日期:2016-04-01 00:00:00

  • Genome editing comes of age.

    abstract::Genome editing harnesses programmable nucleases to cut and paste genetic information in a targeted manner in living cells and organisms. Here, I review the development of programmable nucleases, including zinc finger nucleases (ZFNs), TAL (transcription-activator-like) effector nucleases (TALENs) and CRISPR (cluster o...

    journal_title:Nature protocols

    pub_type: 杂志文章,评审

    doi:10.1038/nprot.2016.104

    authors: Kim JS

    更新日期:2016-09-01 00:00:00

  • Targeted bulk-loading of fluorescent indicators for two-photon brain imaging in vivo.

    abstract::One of the challenges for modern neuroscience is to understand the rules of concerted neuronal function in vivo. This question can be addressed using noninvasive high-resolution imaging techniques like two-photon microscopy. This protocol describes a versatile approach for in vivo two-photon calcium imaging of neural ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.58

    authors: Garaschuk O,Milos RI,Konnerth A

    更新日期:2006-01-01 00:00:00

  • Analyzing bacterial extracellular vesicles in human body fluids by orthogonal biophysical separation and biochemical characterization.

    abstract::Gram-negative and Gram-positive bacteria release a variety of membrane vesicles through different formation routes. Knowledge of the structure, molecular cargo and function of bacterial extracellular vesicles (BEVs) is primarily obtained from bacteria cultured in laboratory conditions. BEVs in human body fluids have b...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0236-5

    authors: Tulkens J,De Wever O,Hendrix A

    更新日期:2020-01-01 00:00:00

  • 3D computational reconstruction of tissues with hollow spherical morphologies using single-cell gene expression data.

    abstract::Single-cell gene expression analysis has contributed to a better understanding of the transcriptional heterogeneity in a variety of model systems, including those used in research in developmental, cancer and stem cell biology. Nowadays, technological advances facilitate the generation of large gene expression data se...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.022

    authors: Durruthy-Durruthy R,Gottlieb A,Heller S

    更新日期:2015-03-01 00:00:00

  • Analysis of mutational spectra by denaturing capillary electrophoresis.

    abstract::The point mutational spectrum over nearly any 75- to 250-bp DNA sequence isolated from cells, tissues or large populations may be discovered using denaturing capillary electrophoresis (DCE). A modification of the standard DCE method that uses cycling temperature (e.g., +/-5 degrees C), CyDCE, permits optimal resolutio...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.79

    authors: Ekstrøm PO,Khrapko K,Li-Sucholeiki XC,Hunter IW,Thilly WG

    更新日期:2008-01-01 00:00:00

  • Frozen competent yeast cells that can be transformed with high efficiency using the LiAc/SS carrier DNA/PEG method.

    abstract::Here we describe a protocol for the production of frozen competent yeast cells that can be transformed with high efficiency using the lithium acetate/single-stranded carrier DNA/PEG method. This protocol allows the production of highly competent yeast cells that can be frozen and used at a later date and is especially...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.17

    authors: Gietz RD,Schiestl RH

    更新日期:2007-01-01 00:00:00

  • A plate-based electrochromic approach for the high-throughput detection of electrochemically active bacteria.

    abstract::Electrochemically active bacteria (EAB) have the ability to transfer electrons to electron acceptors located outside the cell, and they are widely present in diverse environments. In spite of their important roles in geochemical cycles, environmental remediation and electricity generation, so far, only a limited numbe...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.173

    authors: Yuan SJ,Li WW,Cheng YY,He H,Chen JJ,Tong ZH,Lin ZQ,Zhang F,Sheng GP,Yu HQ

    更新日期:2014-01-01 00:00:00

  • Reconstitution of the cell cycle-regulated Golgi disassembly and reassembly in a cell-free system.

    abstract::The Golgi apparatus undergoes extensive disassembly during mitosis and reassembly in post-mitotic daughter cells. This process has been mimicked in vitro by treating Golgi membranes with mitotic and interphase cytosol. To determine the minimal machinery that controls the morphological change, we have developed a defin...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2010.38

    authors: Tang D,Xiang Y,Wang Y

    更新日期:2010-04-01 00:00:00

  • Application of cationic conjugated polymers in microarrays using label-free DNA targets.

    abstract::A fluorescence-based microarray technique that does not require target DNA labeling is detailed. This 'label-free' approach utilizes a cationic, water-soluble conjugated polymer PFBT (poly[9,9'-bis(6''-(N,N,N-trimethylammonium)hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide]), and neutral PNA (peptide nuc...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.307

    authors: Sun C,Gaylord BS,Hong JW,Liu B,Bazan GC

    更新日期:2007-01-01 00:00:00

  • Microfluidic, marker-free isolation of circulating tumor cells from blood samples.

    abstract::The ability to isolate and analyze rare circulating tumor cells (CTCs) has the potential to further our understanding of cancer metastasis and enhance the care of cancer patients. In this protocol, we describe the procedure for isolating rare CTCs from blood samples by using tumor antigen-independent microfluidic CTC-...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2014.044

    authors: Karabacak NM,Spuhler PS,Fachin F,Lim EJ,Pai V,Ozkumur E,Martel JM,Kojic N,Smith K,Chen PI,Yang J,Hwang H,Morgan B,Trautwein J,Barber TA,Stott SL,Maheswaran S,Kapur R,Haber DA,Toner M

    更新日期:2014-03-01 00:00:00

  • A whole-tissue RNA-seq toolkit for organism-wide studies of gene expression with PME-seq.

    abstract::The immune system operates at the scale of the whole organism in mammals. We currently lack experimental approaches to systematically track and study organism-wide molecular processes in mice. Here we describe an integrated toolkit for measuring gene expression in whole tissues, 3-prime mRNA extension sequencing, that...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0291-y

    authors: Pandey S,Takahama M,Gruenbaum A,Zewde M,Cheronis K,Chevrier N

    更新日期:2020-04-01 00:00:00

  • Derivation and maintenance of human embryonic stem cells from poor-quality in vitro fertilization embryos.

    abstract::Human embryonic stem (hES) cells are self-renewing, pluripotent cells that are valuable research tools and hold promise for use in regenerative medicine. Most hES cell lines are derived from cryopreserved human embryos that were created during in vitro fertilization (IVF) and are in excess of clinical need. Embryos th...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.60

    authors: Lerou PH,Yabuuchi A,Huo H,Miller JD,Boyer LF,Schlaeger TM,Daley GQ

    更新日期:2008-01-01 00:00:00

  • Characterization of bacterial spore germination using phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers.

    abstract::This protocol describes a method combining phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers to characterize the germination of single bacterial spores. The characterization consists of the following steps: (i) loading heat-activated dormant spores into a temperature-controlled micros...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2011.307

    authors: Kong L,Zhang P,Wang G,Yu J,Setlow P,Li YQ

    更新日期:2011-05-01 00:00:00

  • In vivo two-photon imaging of sensory-evoked dendritic calcium signals in cortical neurons.

    abstract::Neurons in cortical sensory regions receive modality-specific information through synapses that are located on their dendrites. Recently, the use of two-photon microscopy combined with whole-cell recordings has helped to identify visually evoked dendritic calcium signals in mouse visual cortical neurons in vivo. The c...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2010.169

    authors: Jia H,Rochefort NL,Chen X,Konnerth A

    更新日期:2011-01-01 00:00:00

  • A human intestinal M-cell-like model for investigating particle, antigen and microorganism translocation.

    abstract::The specialized microfold cells (M cells) in the follicle-associated epithelium (FAE) of intestinal Peyer's patches serve as antigen-sampling cells of the intestinal innate immune system. Unlike 'classical' enterocytes, they are able to translocate diverse particulates without digesting them. They act as pathways for ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2017.041

    authors: Beloqui A,Brayden DJ,Artursson P,Préat V,des Rieux A

    更新日期:2017-07-01 00:00:00

  • Six alternative proteases for mass spectrometry-based proteomics beyond trypsin.

    abstract::Protein digestion using a dedicated protease represents a key element in a typical mass spectrometry (MS)-based shotgun proteomics experiment. Up to now, digestion has been predominantly performed with trypsin, mainly because of its high specificity, widespread availability and ease of use. Lately, it has become appar...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2016.057

    authors: Giansanti P,Tsiatsiani L,Low TY,Heck AJ

    更新日期:2016-05-01 00:00:00

  • Slide preparation for single-cell-resolution imaging of fluorescent proteins in their three-dimensional near-native environment.

    abstract::In recent years, many mouse models have been developed to mark and trace the fate of adult cell populations using fluorescent proteins. High-resolution visualization of such fluorescent markers in their physiological setting is thus an important aspect of adult stem cell research. Here we describe a protocol to produc...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2011.365

    authors: Snippert HJ,Schepers AG,Delconte G,Siersema PD,Clevers H

    更新日期:2011-07-28 00:00:00

  • Generation of lung organoids from human pluripotent stem cells in vitro.

    abstract::The lung epithelium is derived from the endodermal germ layer, which undergoes a complex series of endoderm-mesoderm-mediated signaling events to generate the final arborized network of conducting airways (bronchi, bronchioles) and gas-exchanging units (alveoli). These stages include endoderm induction, anterior-poste...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-018-0104-8

    authors: Miller AJ,Dye BR,Ferrer-Torres D,Hill DR,Overeem AW,Shea LD,Spence JR

    更新日期:2019-02-01 00:00:00

  • Population-specific genotype imputations using minimac or IMPUTE2.

    abstract::In order to meaningfully analyze common and rare genetic variants, results from genome-wide association studies (GWASs) of multiple cohorts need to be combined in a meta-analysis in order to obtain enough power. This requires all cohorts to have the same single-nucleotide polymorphisms (SNPs) in their GWASs. To this e...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.077

    authors: van Leeuwen EM,Kanterakis A,Deelen P,Kattenberg MV,Genome of the Netherlands Consortium.,Slagboom PE,de Bakker PI,Wijmenga C,Swertz MA,Boomsma DI,van Duijn CM,Karssen LC,Hottenga JJ

    更新日期:2015-09-01 00:00:00

  • Multiparameter screening method for developing optimized red-fluorescent proteins.

    abstract::Genetically encoded fluorescent proteins (FPs) are highly utilized in cell biology research to study proteins of interest or signal processes using biosensors. To perform well in specific applications, these FPs require a multitude of tailored properties. It is for this reason that they need to be optimized by using m...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0250-7

    authors: Bindels DS,Postma M,Haarbosch L,van Weeren L,Gadella TWJ Jr

    更新日期:2020-02-01 00:00:00

  • Post-translational mutagenesis for installation of natural and unnatural amino acid side chains into recombinant proteins.

    abstract::Methods for installing natural and unnatural amino acids and their modifications into proteins in a benign and precise manner are highly sought-after in protein science. Here we describe a protocol for 'post-translational mutagenesis' that enables the programmed installation of protein side chains through the use of r...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2017.087

    authors: Wright TH,Davis BG

    更新日期:2017-10-01 00:00:00

  • Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine.

    abstract::To uncover the function of and interplay between the mammalian cytosine modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), new techniques and advances in current technology are needed. To this end, we have developed oxidative bisulfite sequencing (oxBS-seq), which can quantitatively locate 5mC an...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.115

    authors: Booth MJ,Ost TW,Beraldi D,Bell NM,Branco MR,Reik W,Balasubramanian S

    更新日期:2013-10-01 00:00:00

  • In-gel stable isotope labeling for relative quantification using mass spectrometry.

    abstract::Although differences in protein staining intensity can often be visualized by difference gel electrophoresis, abundant proteins can obscure less abundant proteins, and quantification of post-translational modifications is difficult. We present a protocol for quantifying changes in the abundance of a specific protein o...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.7

    authors: Asara JM,Zhang X,Zheng B,Maroney LA,Christofk HR,Wu N,Cantley LC

    更新日期:2006-01-01 00:00:00

  • Probing 2-dimensional protein-protein interactions on model membranes.

    abstract::This protocol describes an in vitro approach for measuring the kinetics and affinities of interactions between membrane-anchored proteins. This method is particularly established for dissecting the interaction dynamics of cytokines with their receptor subunits. For this purpose, the receptor subunits are tethered in a...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.270

    authors: Gavutis M,Lata S,Piehler J

    更新日期:2006-01-01 00:00:00

  • Identification and quantification of aminophospholipid molecular species on the surface of apoptotic and activated cells.

    abstract::This protocol measures externalization of aminophospholipids (APLs) to the outside of the plasma membrane using mass spectrometry (MS). APL externalization occurs in numerous events, and it is relevant for transplant medicine, immunity and cancer. In this protocol, externalized APLs are chemically modified by using a ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.163

    authors: Thomas CP,Clark SR,Hammond VJ,Aldrovandi M,Collins PW,O'Donnell VB

    更新日期:2014-01-01 00:00:00

  • Gene function analysis in complex data sets using ErmineJ.

    abstract::ErmineJ is software for the analysis of functionally interesting patterns in large gene lists drawn from gene expression profiling data or other high-throughput genomics studies. It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. It allo...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2010.78

    authors: Gillis J,Mistry M,Pavlidis P

    更新日期:2010-06-01 00:00:00