Lac/Tet dual-inducible system functions in mammalian cell lines

New Dual Inducible Cellular Model to Investigate Temporal Control of Oncogenic Cooperating Genes

The study of cooperating genes in cancer can lead to mechanistic understanding and identifying potential therapeutic targets. To facilitate these types of studies, we developed a new dual-inducible system utilizing the tetracycline- and cumate-inducible systems driving HES3 and the PAX3::FOXO1 fusion-oncogene, respectively, as cooperating genes from fusion-positive rhabdomyosarcoma. With this new model, we can independently induce expression of either HES3 or PAX3::FOXO1, as well as simultaneously induce expression of both genes. This new model will allow us to further investigate the cooperation between HES3 and PAX3::FOXO1 including the temporal requirements for genetic cooperation. This dual-inducible model can be adapted for any cooperating genes, allowing for independent, simultaneous, or temporally controlled gene expression.

Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications

Synthetic biologists use engineering principles to design and construct genetic circuits for programming cells with novel functions. A bottom-up approach is commonly used to design and construct genetic circuits by piecing together functional modules that are capable of reprogramming cells with novel behavior. While genetic circuits control cell operations through the tight regulation of gene expression, a diverse array of environmental factors within the extracellular space also has a significant impact on cell behavior. This extracellular space offers an addition route for synthetic biologists to apply their engineering principles to program cell-responsive modules within the extracellular space using biomaterials. In this review, we discuss how taking a bottom-up approach to build genetic circuits using DNA modules can be applied to biomaterials for controlling cell behavior from the extracellular milieu. We suggest that, by collectively controlling intrinsic and extrinsic signals in synthetic biology and biomaterials, tissue engineering outcomes can be improved.

Versatile approach for functional analysis of human proteins and efficient stable cell line generation using FLP-mediated recombination system

Deciphering a function of a given protein requires investigating various biological aspects. Usually, the protein of interest is expressed with a fusion tag that aids or allows subsequent analyses. Additionally, downregulation or inactivation of the studied gene enables functional studies. Development of the CRISPR/Cas9 methodology opened many possibilities but in many cases it is restricted to non-essential genes. Recombinase-dependent gene integration methods, like the Flp-In system, are very good alternatives. The system is widely used in different research areas, which calls for the existence of compatible vectors and efficient protocols that ensure straightforward DNA cloning and generation of stable cell lines. We have created and validated a robust series of 52 vectors for streamlined generation of stable mammalian cell lines using the FLP recombinase-based methodology. Using the sequence-independent DNA cloning method all constructs for a given coding-sequence can be made with just three universal PCR primers. Our collection allows tetracycline-inducible expression of proteins with various tags suitable for protein localization, FRET, bimolecular fluorescence complementation (BiFC), protein dynamics studies (FRAP), co-immunoprecipitation, the RNA tethering assay and cell sorting. Some of the vectors contain a bidirectional promoter for concomitant expression of miRNA and mRNA, so that a gene can be silenced and its product replaced by a mutated miRNA-insensitive version. Our toolkit and protocols have allowed us to create more than 500 constructs with ease. We demonstrate the efficacy of our vectors by creating stable cell lines with various tagged proteins (numatrin, fibrillarin, coilin, centrin, THOC5, PCNA). We have analysed transgene expression over time to provide a guideline for future experiments and compared the effectiveness of commonly used inducers for tetracycline-responsive promoters. As proof of concept we examined the role of the exoribonuclease XRN2 in transcription termination by RNAseq.

Tools and applications in synthetic biology

Advances in synthetic biology have enabled the engineering of cells with genetic circuits in order to program cells with new biological behavior, dynamic gene expression, and logic control. This cellular engineering progression offers an array of living sensors that can discriminate between cell states, produce a regulated dose of therapeutic biomolecules, and function in various delivery platforms. In this review, we highlight and summarize the tools and applications in bacterial and mammalian synthetic biology. The examples detailed in this review provide insight to further understand genetic circuits, how they are used to program cells with novel functions, and current methods to reliably interface this technology in vivo; thus paving the way for the design of promising novel therapeutic applications.

Synthetic mechanobiology: engineering cellular force generation and signaling

Mechanobiology seeks to understand and control mechanical and related biophysical communication between cells and their surroundings. While experimental efforts in this field have traditionally emphasized manipulation of the extracellular force environment, a new suite of approaches has recently emerged in which cell phenotype and signaling are controlled by directly engineering the cell itself. One route is to control cell behavior by modulating gene expression using conditional promoters. Alternatively, protein activity can be actuated directly using synthetic protein ligands, chemically induced protein dimerization, optogenetic strategies, or functionalized magnetic nanoparticles. Proof-of-principle studies are already demonstrating the translational potential of these approaches, and future technological development will permit increasingly precise control over cell mechanobiology and improve our understanding of the underlying signaling events.

Simultaneous and independent tuning of RhoA and Rac1 activity with orthogonally inducible promoters

The GTPases RhoA and Rac1 are key regulators of cell spreading, adhesion, and migration, and they exert distinct effects on the actin cytoskeleton. While RhoA classically stimulates stress fiber assembly and contraction, Rac1 promotes branched actin polymerization and membrane protrusion. These competing influences are reinforced by antagonistic crosstalk between RhoA and Rac1, which has complicated efforts to identify the specific mechanisms by which each GTPase regulates cell behavior. We therefore wondered whether RhoA and Rac1 are intrinsically coupled or whether they can be manipulated independently. To address this question, we placed constitutively active (CA) RhoA under a doxycycline-inducible promoter and CA Rac1 under an orthogonal cumate-inducible promoter, and we stably introduced both constructs into glioblastoma cells. We found that doxycycline addition increased RhoA activity without altering Rac1, and similarly cumate addition increased Rac1 activity without altering RhoA. Furthermore, co-expression of both mutants enabled high activation of RhoA and Rac1 simultaneously. When cells were cultured on collagen hydrogels, RhoA activation prevented cell spreading and motility, whereas Rac1 activation stimulated migration and dynamic cell protrusions. Interestingly, high activation of both GTPases induced a third phenotype, in which cells migrated at intermediate speeds similar to control cells but also aggregated into large, contractile clusters. In addition, we demonstrate dynamic and reversible switching between high RhoA and high Rac1 phenotypes. Overall, this approach represents a unique way to access different combinations of RhoA and Rac1 activity levels in a single cell and may serve as a valuable tool for multiplexed dissection and control of mechanobiological signals.

Three-dimensional patterning of multiple cell populations through orthogonal genetic control of cell motility

The ability to independently assemble multiple cell types within a three-dimensional matrix would be a powerful enabling tool for modeling and engineering complex tissues. Here we introduce a strategy to dynamically pattern distinct subpopulations of cells through genetic regulation of cell motility. We first describe glioma cell lines that were genetically engineered to stably express constitutively active or dominant negative Rac1 GTPase mutants under the control of either a doxycycline-inducible or cumate-inducible promoter. We culture each population as multicellular spheroids and show that by adding or withdrawing the appropriate inducer at specific times, we can control the timing and extent of Rac1-dependent cell migration into three-dimensional collagen matrices. We then report results with mixed spheroids in which one subpopulation of cells expresses dominant negative Rac1 under a doxycycline-inducible promoter and the other expresses dominant negative Rac1 under a cumate-inducible promoter. Using this system, we demonstrate that doxycycline and cumate addition suppress Rac1-dependent motility in a subpopulation-specific and temporally-controlled manner. This allows us to orthogonally control the motility of each subpopulation and spatially assemble the cells into radially symmetric three-dimensional patterns through the synchronized addition and removal of doxycycline and cumate. This synthetic biology-inspired strategy offers a novel means of spatially organizing multiple cell populations in conventional matrix scaffolds and complements the emerging suite of technologies that seek to pattern cells by engineering extracellular matrix properties.

Magnetic resonance imaging and spectroscopy of transgenic models of cancer

The complexity of cancer, where a single genetic alteration can have multiple functional effects, makes it a fascinating but humbling disease to study, and the necessity of investigating it in its entirety is more imperative than ever before. Advances in transgene technology have made it possible to create cancer cells, or mice with specific genetic alterations, and the application of an array of both functional and molecular non-invasive MR methods to these transgenic cancer cells and mice to characterize their phenotypic traits is revolutionizing our understanding of cancer. With the establishment of multi-modality molecular imaging centers within barrier or pathogen-free facilities, multi-parametric and multi-modality imaging of transgenic mouse models of human cancer are becoming increasingly prevalent. In this review, we outline some of the methods currently available for generating transgenic mice and cancer cell lines. We also present examples of the application of MR methods to transgenic models that are providing novel insights into the molecular and functional characteristics of cancer and are leading to an era of "non-invasive phenotyping" of the effects of specific molecular alterations in cancer.

Inducible functional expression of Bcl-2 in human astrocytes derived from NTera-2 cells

Astrocytes provide structural support for neurons and may also play important roles in both neuroprotection and neurodegeneration. We, here report that human astrocytes derived from on NTera-2 (NT2) cell line expressing a functional anti-apoptotic protein bcl-2 under the control of a tetracycline responsive promoter using the Tet-On and Tet-Off expression systems. NT2 cells were transfected with the Tet On or Tet Off vectors followed by pTRE carrying human bcl-2. Drug resistant cells were differentiated into astrocytes under retinoic acid exposure. These astrocyte lines were found to express astrocyte specific markers such glial fibrillary acidic protein and chemokine receptors (CCR5, CXCR4) but not CCR3 and CD4. Furthermore, NT2 astrocytes expressing bcl-2 showed rapid response to doxycycline presence in the Tet On and Tet off system. The inducible expression of bcl-2 was found to be tightly regulated by doxycycline concentration in the NT2 astrocytes. We also showed that the induction of bcl-2 expression prevented NT2 astrocytes from camptothecin-induced cellular damage. These results indicate that this system may be useful for the study of specific effects of bcl-2 gene expression on astrocyte function(s) and cellular damage.

Modulation of translation-initiation in CHO-K1 cells by rapamycin-induced heterodimerization of engineered eIF4G fusion proteins

Translation-initiation is a predominant checkpoint in mammalian cells which controls protein synthesis and fine-tunes the flow of information from gene to protein. In eukaryotes, translation-initiation is typically initiated at a 7-methyl-guanylic acid cap posttranscriptionally linked to the 5' end of mRNAs. Alternative cap-independent translation-initiation involves 5' untranslated regions (UTR) known as internal ribosome entry sites, which adopt a particular secondary structure. Translation-initiating ribosome assembly at cap or IRES elements is mediated by a multiprotein complex of which the initiation factor 4F (eIF4F) consisting of eIF4A (helicase), eIF4E (cap-binding protein), and eIF4G is a major constituent. eIF4G is a key target of picornaviral protease 2A, which cleaves this initiation factor into eIF4G(Delta) and (Delta)eIF4G to redirect the cellular translation machinery exclusively to its own IRES-containing transcripts. We have designed a novel translation control system (TCS) for conditional as well as adjustable translation of cap- and IRES-dependent transgene mRNAs in mammalian cells. eIF4G(Delta) and (Delta)eIF4G were fused C- and N-terminally to the FK506-binding protein (FKBP) and the FKBP-rapamycin-binding domain (FRB) of the human FKBP-rapamycin-associated protein (FRAP), respectively. Rapamycin-induced heterodimerization of eIF4G(Delta)-FKBP and FRB-(Delta)eIF4G fusion proteins reconstituted a functional chimeric elongation factor 4G in a dose-dependent manner. Rigorous quantitative expression analysis of cap- and IRES-dependent SEAP- (human placental secreted alkaline phosphatase) and luc- (Photinus pyralis luciferase) encoding reporter constructs confirmed adjustable translation control and revealed increased production of desired proteins in response to dimerization-induced heterologous eIF4G in Chinese hamster ovary (CHO-K1) cells.

Dual-regulated expression technology: a new era in the adjustment of heterologous gene expression in mammalian cells

BACKGROUND

On the basis of the compatible streptogramin- and tetracycline-responsive expression systems, a series of dual-regulated expression systems have been established for use in sophisticated biopharmaceutical manufacturing, advanced gene therapy, and tissue engineering.

METHODS

Dual-regulated expression concepts enable streptogramin- and tetracycline-responsive control of two different (sets of) transgenes (multi-regulated multigene metabolic engineering), dual-autoregulated expression configurations for one-step chromosomal integration of two antibiotic-adjustable expression units, and artificial regulatory cascades for multi-level regulation of transgenes and optimized integration of molecular interventions into mammalian regulatory networks.

RESULTS

This report describes the construction and testing of a family of dual-regulated expression vectors which are compatible with the pTRIDENT vector construction kit, and, in some cases, adapted for retroviral expression technology enabling straightforward transduction of difficult-to-transfect cell lines such as primary cells and stem cells.

CONCLUSIONS

Dual-regulated expression technology will probably become of prime interest for a variety of therapeutic applications, including biopharmaceutical manufacturing, gene therapy, and tissue engineering.