Inducible expression based on regulated recombination: a single vector strategy for stable expression in cultured cells

A "Hit and Run" Approach to Inducible Direct Reprogramming of Astrocytes to Neural Stem Cells

Temporal and spatial control of gene expression can be achieved using an inducible system as a fundamental tool for regulated transcription in basic, applied and eventually in clinical research. We describe a novel “hit and run” inducible direct reprogramming approach. In a single step, 2 days post-transfection, transiently transfected Sox2^FLAG under the Leu3p-αIPM inducible control (iSox2) triggers the activation of endogenous Sox2, redirecting primary astrocytes into abundant distinct nestin-positive radial glia cells. This technique introduces a unique novel tool for safe, rapid and efficient reprogramming amendable to regenerative medicine.

Dre recombinase, like Cre, is a highly efficient site-specific recombinase in E. coli, mammalian cells and mice

Tyrosine site-specific recombinases (SSRs) including Cre and FLP are essential tools for DNA and genome engineering. Cre has long been recognized as the best SSR for genome engineering, particularly in mice. Obtaining another SSR that is as good as Cre will be a valuable addition to the genomic toolbox. To this end, we have developed and validated reagents for the Dre-rox system. These include an Escherichia coli-inducible expression vector based on the temperature-sensitive pSC101 plasmid, a mammalian expression vector based on the CAGGs promoter, a rox-lacZ reporter embryonic stem (ES) cell line based on targeting at the Rosa26 locus, the accompanying Rosa26-rox reporter mouse line, and a CAGGs-Dre deleter mouse line. We also show that a Dre-progesterone receptor shows good ligand-responsive induction properties. Furthermore, we show that there is no crossover recombination between Cre-rox or Dre-loxP. Hence, we add another set of efficient tools to the genomic toolbox, which will enable the development of more sophisticated mouse models for the analysis of gene function and disease.

Transcription factors and the genetic organization of brain stem respiratory neurons

Breathing is a genetically determined behavior generated by neurons in the brain stem. Transcription factors, in part, determine the basic developmental identity of neurons, but the relationships between these genes and the neural populations generating and modulating respiration are unclear. The diversity of brain stem populations has been proposed to result from a combinatorial code of transcription factor expression corresponding to the anterior-posterior (A-P) and dorsal-ventral (D-V) location of a neuron's birth. I provide a schematic of transcription factor coding identifying at least 15 genetically distinct D-V subdivisions of brain stem neurons that, combined with A-P patterning, may provide a genetic organization of the brain stem in general, with the eventual goal of describing respiratory populations in particular. Using a combination of fate mapping in transgenic mouse lines and immunohistochemistry, we confirm the parabrachial nuclei are derived from a subset of Atoh1 expression progenitor neurons. I hypothesize the Kölliker-Fuse nucleus can be uniquely defined in the neonate mouse by the coexpression of the transcription factor FoxP2 in Atoh1-derived neurons of rhombomere 1.

Floxed reporter genes: Flow-cytometric selection of clonable cells expressing high levels of a target gene after tamoxifen-regulated Cre-loxP recombination

Tamoxifen treatment allows MerCreMer fusion recombinase to localize to the nucleus where MerCreMer can excise a floxed inhibitory DNA segment, thereby activating the expression of a downstream gene. This excision is irreversible, and it is therefore difficult to predict which non-activated clones will express the gene at high levels after recombination. We transfected a vector using HLA-A2.1 as floxed inhibitory DNA element and its expression level as surrogate marker predicting future expression of the attenuated downstream target gene. The target gene encoded an EGFP-linked fusion protein. In the unsorted population, 6% of the cells expressed the transfected target gene after recombination and less than 10-fold higher than the population before recombination. However after flow-cytometric selection for high HLA-A2.1 expression, 47% of the cells expressed the target gene after recombination and at levels 37-fold higher than the sorted population before recombination. 58% of the clones were capable of expressing the fusion protein and some over 200-fold above background of untransfected cells and greater than 20-fold higher levels of expression than before recombination. We describe an efficient method to select for clones expressing high levels of a target gene after tamoxifen regulated Cre-loxP recombination. Other floxed reporter genes should be equally useful.

Engineering embryonic stem cells with recombinase systems

The combined use of site-specific recombination and gene targeting or trapping in embryonic stem cells (ESCs) has resulted in the emergence of technologies that enable the induction of mouse mutations in a prespecified temporal and spatially restricted manner. Their large-scale implementation by several international mouse mutagenesis programs will lead to the assembly of a library of ES cell lines harboring conditional mutations in every single gene of the mouse genome. In anticipation of this unprecedented resource, this chapter will focus on site-specific recombination strategies and issues pertinent to ESCs and mice. The upcoming ESC resource and the increasing sophistication of site-specific recombination technologies will greatly assist the functional annotation of the human genome and the animal modeling of human disease.

Genetic changes occurring in established tumors rapidly stimulate new antibody responses

Cancer patients and tumor-bearing mice possess serum antibodies that recognize antigens expressed by cancer cells at the time of diagnosis. After diagnosis, cancers progress to more aggressive stages, most often by acquiring new genetic changes that can give rise to new proteins, some of which are antigenic. However, at these relatively later stages of tumor growth, it remains unclear whether, when, and how a host can generate de novo antibody responses against these newly appearing tumor antigens. To this end, we used a tamoxifen-regulated Cre-loxP system, MerCreMer, to induce genetic recombination in cancer cells of well-established tumors, resulting in increased enhanced green fluorescence protein (EGFP) expression. These late tumor-bearing mice generated specific IgG antibodies against EGFP within 3 wk after antigen induction. Mice generated these antibody responses in the presence of preexisting anti-tumor antibody responses. Preexisting CD4(+) T cell responses to already expressed tumor antigens likely enhanced antibody responses to the induced EGFP antigen. By analogy, new antibody responses in cancer patients may identify genetic changes occurring in a growing tumor and indicate imminent tumor progression.

Regulated expression of diphtheria toxin in prostate cancer cells

Despite their known potential for effectively killing cells, the therapeutic use of plant and bacterial toxins for the treatment of cancer has been slow to enter the clinical setting. This has been due in large part to the lack of gene regulatory elements that control expression of highly toxic genes in a sufficiently tight manner, such that the toxins are only expressed in specific target cells. "Leaky" promoters result in unwanted and harmful cell death. In this study, we tested a novel gene therapy strategy aimed at expressing diphtheria toxin (DT-A) in androgen-independent prostate cancer cells that express the protein BCL2. This strategy relies on both transcriptional regulation and inducibly regulated DNA recombination mediated by the site-directed Flp recombinase to control expression of the toxin. Adenoviruses are used to introduce the genetic elements required for this approach into cultured cells and xenografts. Administration of 4-hydroxytamoxifen, resulting in recombination and expression of the toxin, effectively kills the cancer cells. Our results suggest that following androgen ablation therapy for the treatment of prostate cancer, use of a regulated recombination system to target expression of DT-A to androgen-independent cancer cells would be an effective way to arrest the development of recurrent tumors.

PG13 packaging cells produce recombinant retroviruses carrying a diphtheria toxin mutant which kills cancer cells

The development of suicide gene therapy with gene products that are directly toxic to cells, such as the A subunit of diphtheria toxin (DT-A), has been hampered by the difficulty of engineering recombinant viruses. DT-A is a strong inhibitor of protein synthesis that acts by ADP-ribosylating elongation factor 2, and a low level of DT-A expression in virus producer cells prevents the production of recombinant virus. We analyzed here the natural resistance of packaging cells to DT-A toxicity, and we report that PG13 and PA317 packaging cell lines are resistant to H21G, a DT-A mutant. PG13 cells produce recombinant H21G virus that efficiently kills a variety of human tumor cells. Our finding indicates that PG13 packaging cells provide a new potential for the development of DT-A-based suicide gene therapy.

Functionally orthogonal ligand-receptor pairs for the selective regulation of gene expression generated by manipulation of charged residues at the ligand-receptor interface of ER alpha and ER beta

The reengineering of protein-small molecule interfaces represents a powerful tool of chemical biology. For many applications it is necessary to engineer receptors so that they do not interact with their endogenous ligands but are highly responsive to designed ligand analogues, which in turn do not interact with endogenous proteins. The chemical design strategy used to reengineer protein-small molecule interfaces is particularly challenging for interfaces involving relatively plastic receptor binding sites and therefore presents a unique challenge in molecular design. In this study we explore the scope and limitations of a new strategy for manipulating polar/charged residues across the ligand receptor interface of estradiol (E2) and the estrogen receptor (ER). Carboxylate-functionalized E2 analogues can activate ER alpha(Glu353-->Ala) and ER beta(Glu305-->Ala) with very large selectivites, demonstrating that this design strategy is extendable to other members of the steroid hormone receptor family. Neutral E2 analogues were found to complement ER alpha(E353A) with similar potencies but with generally lower selectivities. This suggests that the high selectivity observed with ligand-receptor pairs generated by exchanging charged residues across ligand-receptor interfaces is only due in part to their complementary shapes and that appropriate introduction of charged functionality on the ligand can provide substantial enhancement of selectivity by decreasing the engineered ligands affinity for the endogenous receptor. Attempts to modify the cationic residues by complementing Arg394-->Ala or Arg394-->Glu were not successful.

FLP and Cre recombinase function in Xenopus embryos

The use of the site-specific DNA recombinases FLP and Cre is well-established in a broad range of organisms. Here we investigate the applicability of both recombinases to the Xenopus system where they have not been analyzed yet. We show that injection of FLP mRNA triggers the excision of an FLP recombination target (FRT)-flanked green fluorescent protein (GFP) sequence in a coinjected reporter construct inducing the expression of a downstream beta-galactosidase gene (lacZ). The FLP-mediated gene activation can be controlled in Xenopus embryos by injecting a mRNA encoding a fusion of FLP to the mutant ligand binding domain of the human estrogen receptor whose activity is dependent on 4-hydroxytamoxifen. We also demonstrate that a Cre reporter injected into fertilized eggs is fully recombined by Cre recombinase before zygotic gene transcription initiates. Our results indicate that in Xenopus embryos Cre is more effective than FLP in recombining a given quantity of reporter molecules. Finally, we present FLP-inducible double reporter systems encoding two fluorescence proteins (EYFP, ECFP, DsRed or GFP). These novel gene expression systems enable the continuous analysis of two reporter activities within living embryos and are expected to allow cell-lineage studies based on recombinase-mediated DNA rearrangement in transgenic Xenopus lines.

Selective regulation of gene expression by an orthogonal estrogen receptor–ligand pair created by polar-group exchange

BACKGROUND

The nuclear and steroid hormone receptors function as ligand-dependent transcriptional regulators in eukaryotes. Hormone receptors have been engineered to selectively respond to synthetic ligands and used as remote regulators of gene expression for the study of gene function and as potential regulators of gene therapies.

RESULTS

In this work, a new ligand-receptor engineering strategy called 'polar-group exchange' is used to create a mutant form of the estrogen receptor, ER(Glu353-->Ala), which lacks a carboxyl group critical for high-affinity binding of estradiol, but is able to transactivate in response to nanomolar concentrations of a carboxylate-functionalized estrogen analog, ES8. ES8 activates ER(Glu353-->Ala) at concentrations that do not appreciably activate the 'wild-type' receptor ER(wt). Two similar carboxylate-functionalized ligands, ES6 and ES7, do not induce transactivation function. Similar selectivities are observed in ligand-binding assays in vitro, which follow the trends predicted by molecular modeling.

CONCLUSION

Polar-group exchange is an effective strategy for rationally engineering ligand-receptor pairs. The ER(E353A)/ES8 ligand-receptor pair should constitute a unique and functionally orthogonal ligand-dependent transcriptional regulator.

Controlling gene expression in yeast by inducible site-specific recombination

An intron module was developed for Saccharomyces cerevisiae that imparts conditional gene regulation. The kanMX marker, flanked by loxP sites for the Cre recombinase, was embedded within the ACT1 intron and the resulting module was targeted to specific genes by PCR-mediated gene disruption. Initially, recipient genes were inactivated because the loxP-kanMX-loxP cassette prevented formation of mature transcripts. However, expression was restored by Cre-mediated site-specific recombination, which excised the loxP-kanMX-loxP cassette to generate a functional intron that contained a single loxP site. Cre recombinase activity was controlled at the transcriptional level by a GAL1::CRE expression vector or at the enzymatic level by fusing the protein to the hormone-dependent regulatory domain of the estrogen receptor. Negative selection against leaky pre-excision events was achieved by growing cells in modified minimal media that contained geneticin (G418). Advantages of this gene regulation technique, which we term the conditional knock-out approach, are that (i) modified genes are completely inactivated prior to induction, (ii) modified genes are induced rapidly to expression levels that compare to their unmodified counterparts, and (iii) it is easy to use and generally applicable.

Components of vectors for gene transfer and expression in mammalian cells

Progress in diverse scientific fields has been realized partly by the continued refinement of mammalian gene expression vectors. A growing understanding of biological processes now allows the design of vector components to meet specific objectives. Thus, gene expression in a tissue-selective or ubiquitous manner may be accomplished by selecting appropriate promoter/enhancer elements; stabilization of labile mRNAs may be effected through removal of 3' untranslated regions or fusion to heterologous stabilizing sequences; protein targeting to selected tissues or different organelles is carried out using specific signal sequences; fusion moieties effect the detection, enhanced yield, surface expression, prolongation of half-life, and facile purification of recombinant proteins; and careful tailoring of the codon content of heterologous genes enhances protein production from poorly translated transcripts. The use of viral as well as nonviral genetic elements in vectors allows the stable replication of episomal elements without the need for chromosomal integration. The development of baculovirus vectors for both transient and stable gene expression in mammalian cells has expanded the utility of such vectors for a broad range of cell types. Internal ribosome entry sites are now widely used in many applications that require coexpression of different genes. Progress in gene targeting techniques is likely to transform gene expression and amplification in mammalian cells into a considerably less labor-intensive operation. Future progress in the elucidation of eukaryotic protein degradation pathways holds promise for developing methods to minimize proteolysis of specific recombinant proteins in mammalian cells and tissues.

The chicken HPRT gene: a counter selectable marker for the DT40 cell line

We describe the cloning, characterisation and chromosomal mapping of the chicken hprt gene together with the construction of two counter selectable hprt-/- DT40 derived cell lines. One of these cell lines contains a stably integrated gene encoding a conditionally active cre recombinase and thus allows efficient manipulation of targeted loci by site-specific recombination. These cell lines will enhance the utility of the hyper-recombinogenic DT40 cell line as a system for the genetic analysis of cell autonomous functions in vertebrates and as a tool for mammalian chromosome engineering.