Bidirectional expression units enable streptogramin-adjustable gene expression in mammalian cells

Promoters in Pichia pastoris: A Toolbox for Fine-Tuned Gene Expression

This chapter reviews the different promoters used to control gene expression in the yeast Pichia pastoris, mainly for recombinant protein production. It covers natural inducible, derepressed, and constitutive promoters, as well as engineered synthetic/hybrid promoters, orthologous promoters from related yeasts, and emerging bidirectional promoters. Key examples, characteristics, and regulatory mechanisms are discussed for each promoter class. Recent efforts in promoter engineering through rational design, mutagenesis, and computational approaches are also highlighted. Looking ahead, we anticipate further developments that will enhance promoter design for Pichia pastoris. Overall, this comprehensive overview underscores the importance of promoter choice and engineering for fully harnessing Pichia pastoris biotechnological potential.

Toward Tightly Tuned Gene Expression Following Lentiviral Vector Transduction

Lentiviral vectors are versatile tools for gene delivery purposes. While in the earlier versions of retroviral vectors, transgene expression was controlled by the long terminal repeats (LTRs), the latter generations of vectors, including those derived from lentiviruses, incorporate internal constitutive or regulated promoters in order to regulate transgene expression. This allows to temporally and/or quantitatively control transgene expression, which is required for many applications such as for clinical applications, when transgene expression is required in specific tissues and at a specific timing. Here we review the main systems that have been developed for transgene regulated expression following lentiviral gene transfer. First, the induction of gene expression can be triggered either by external or by internal cues. Indeed, these regulated vector systems may harbor promoters inducible by exogenous stimuli, such as small molecules (e.g., antibiotics) or temperature variations, offering the possibility to tune rapidly transgene expression in case of adverse events. Second, expression can be indirectly adjusted by playing on inserted sequence copies, for instance by gene excision. Finally, synthetic networks can be developed to sense specific endogenous signals and trigger defined responses after information processing. Regulatable lentiviral vectors (LV)-mediated transgene expression systems have been widely used in basic research to uncover gene functions or to temporally reprogram cells. Clinical applications are also under development to induce therapeutic molecule secretion or to implement safety switches. Such regulatable approaches are currently focusing much attention and will benefit from the development of other technologies in order to launch autonomously controlled systems.

Engineered bidirectional promoters enable rapid multi-gene co-expression optimization

Numerous synthetic biology endeavors require well-tuned co-expression of functional components for success. Classically, monodirectional promoters (MDPs) have been used for such applications, but MDPs are limited in terms of multi-gene co-expression capabilities. Consequently, there is a pressing need for new tools with improved flexibility in terms of genetic circuit design, metabolic pathway assembly, and optimization. Here, motivated by nature's use of bidirectional promoters (BDPs) as a solution for efficient gene co-expression, we generate a library of 168 synthetic BDPs in the yeast Komagataella phaffii (syn. Pichia pastoris), leveraging naturally occurring BDPs as a parts repository. This library of synthetic BDPs allows for rapid screening of diverse expression profiles and ratios to optimize gene co-expression, including for metabolic pathways (taxadiene, β-carotene). The modular design strategies applied for creating the BDP library could be relevant in other eukaryotic hosts, enabling a myriad of metabolic engineering and synthetic biology applications.

Engineered bidirectional promoters enable rapid multi-gene co-expression optimization

Numerous synthetic biology endeavors require well-tuned co-expression of functional components for success. Classically, monodirectional promoters (MDPs) have been used for such applications, but MDPs are limited in terms of multi-gene co-expression capabilities. Consequently, there is a pressing need for new tools with improved flexibility in terms of genetic circuit design, metabolic pathway assembly, and optimization. Here, motivated by nature’s use of bidirectional promoters (BDPs) as a solution for efficient gene co-expression, we generate a library of 168 synthetic BDPs in the yeast Komagataella phaffii (syn. Pichia pastoris), leveraging naturally occurring BDPs as a parts repository. This library of synthetic BDPs allows for rapid screening of diverse expression profiles and ratios to optimize gene co-expression, including for metabolic pathways (taxadiene, β-carotene). The modular design strategies applied for creating the BDP library could be relevant in other eukaryotic hosts, enabling a myriad of metabolic engineering and synthetic biology applications.

Classic monodirectional promoters are of limited use for multiple gene co-expression. Here the authors generate a library of 168 bidirectional promoters for the yeast K. phaffii (syn. P. pastoris) with diverse expression profiles to optimize metabolic pathway design.

Model-guided combinatorial optimization of complex synthetic gene networks

Constructing gene circuits that satisfy quantitative performance criteria has been a long-standing challenge in synthetic biology. Here, we show a strategy for optimizing a complex three-gene circuit, a novel proportional miRNA biosensor, using predictive modeling to initiate a search in the phase space of sensor genetic composition. We generate a library of sensor circuits using diverse genetic building blocks in order to access favorable parameter combinations and uncover specific genetic compositions with greatly improved dynamic range. The combination of high-throughput screening data and the data obtained from detailed mechanistic interrogation of a small number of sensors was used to validate the model. The validated model facilitated further experimentation, including biosensor reprogramming and biosensor integration into larger networks, enabling in principle arbitrary logic with miRNA inputs using normal form circuits. The study reveals how model-guided generation of genetic diversity followed by screening and model validation can be successfully applied to optimize performance of complex gene networks without extensive prior knowledge.

Chemoprotection by transfer of resistance genes

Dose-limiting toxicity of chemotherapeutic agents, i.e., myelosuppression, can limit their effectiveness. The transfer and expression of drug-resistance genes might decrease the risks associated with acute hematopoietic toxicity. Protection of hematopoietic stem/progenitor cells by transfer of drug-resistance genes provides the possibility of intensification or escalation of antitumor drug doses and consequently an improved therapeutic index. This chapter reviews drug-resistance gene transfer strategies for either myeloprotection or therapeutic gene selection. Selecting candidate drug-resistance gene(s), gene transfer methodology, evaluating the safety and the efficiency of the treatment strategy, relevant in vivo models, and oncoretroviral transduction of human hematopoietic stem/progenitor cells under clinically applicable conditions are described.

Adenovirus-mediated transduction of auto- and dual-regulated transgene expression in mammalian cells

Transduction of therapeutic transgenes using multiply attenuated viral vectors is considered an essential technology for gene therapy scenarios. While first-generation viral transduction systems were engineered for constitutive expression of a single therapeutic transgene, most advanced viral gene-transfer technologies enable regulated expression of several transgenes. Efficient transfer of numerous transgenes enables co-expression of therapeutic transgenes along with marker or selection determinants, production of multi-subunit protein complexes, or combinatorial expression of a particular set of genes to treat multigenic disorders. Likewise, adjustable transcription control is fundamental to adapt therapeutic protein production to the changing daily dosing regimes of a patient, to titrate expression of protein pharmaceuticals into the therapeutic window, and to reverse dosing upon completion of the therapy. Also, conditional transcription dosing has been successfully used for production of difficult-to-express protein therapeutics in biopharmaceutical manufacturing and for sophisticated gene-function analysis in basic research programs. By way of example, we provide detailed design (auto-regulated and binary dual-regulated expression configurations), production (generation, purification, and quality control of transgenic adenovirus particles), and handling (transduction) protocols for adenovirus vectors that enable transduction of mammalian cells for regulated expression of several transgenes.

Pharmacologic transgene control systems for gene therapy

Pharmacologic transgene-expression dosing is considered essential for future gene therapy scenarios. Genetic interventions require precise transcription or translation fine-tuning of therapeutic transgenes to enable their titration into the therapeutic window, to adapt them to daily changing dosing regimes of the patient, to integrate them seamlessly into the patient's transcriptome orchestra, and to terminate their expression after successful therapy. In recent years, decisive progress has been achieved in designing high-precision trigger-inducible mammalian transgene control modalities responsive to clinically licensed and inert heterologous molecules or to endogenous physiologic signals. Availability of a portfolio of compatible transcription control systems has enabled assembly of higher-order control circuitries providing simultaneous or independent control of several transgenes and the design of (semi-)synthetic gene networks, which emulate digital expression switches, regulatory transcription cascades, epigenetic expression imprinting, and cellular transcription memories. This review provides an overview of cutting-edge developments in transgene control systems, of the design of synthetic gene networks, and of the delivery of such systems for the prototype treatment of prominent human disease phenotypes.

Autoregulated, bidirectional and multicistronic gas-inducible mammalian as well as lentiviral expression vectors

We present a novel set of autoregulated, bidirectional and multicistronic mammalian as well as lentiviral expression vectors which enable transgene expression fine-tuning by gaseous acetaldehyde. The acetaldehyde-inducible regulation (AIR) technology capitalizes on Aspergillus nidulans components evolved to convert ethanol into metabolic energy. AIR is based on functional interaction of the fungal transactivator AlcR and AlcR-specific chimeric promoters (P(AIR)) which drive desired transgene expression in mammalian cells only in the presence of gaseous acetaldehyde. We have engineered AIR technology into a variety of different mammalian and lentiviral expression vector systems including (i) a most compact autoregulated expression format harboring alcR and the transgene in a single P(AIR)-driven transcription unit, (ii) a bidirectional P(AIR) derivative supporting expression of two transgenes with strict 1:1 transcription stoichiometry and (iii) a multicistronic expression arrangement providing simultaneous translation of three independent transgenes from a single P(AIR)-controlled transcript. All expression vectors have been validated in Chinese hamster ovary (CHO-K1), baby hamster kidney (BHK-21) and human HeLa cells for gas-inducible (co-)expression of the reporter transgenes such as Bacillus stearothermophilus-derived secreted alpha-amylase (SAMY), human vascular endothelial growth factor 121 (VEGF121), human placental-secreted alkaline phosphatase (SEAP) and Escherichia coli-derived chloramphenicol acetyl-transferase (CAT). The panoply of mammalian/lentiviral vectors presented here provides a robust and versatile expression platform for the first gas-inducible transgene control system which we expect to foster future advances in gene therapy, tissue engineering as well as biopharmaceutical manufacturing.

A novel binary adenovirus-based dual-regulated expression system for independent transcription control of two different transgenes

BACKGROUND

Stringent multitransgene control is a prerequisite for future gene-therapy and tissue-engineering scenarios and requires constant improvements in design to achieve optimal conditional transcription profiles.

METHODS

We have pioneered a variety of recombinant adenoviruses which (i) enable streptogramin-responsive transgene transduction in a compact autoregulated one-virus format, (ii) manage independent streptogramin- and tetracycline-responsive control of two different transgenes from a single divergent expression unit, and (iii) control sense and antisense expression of the human cyclin-dependent kinase inhibitor p27(Kip1) to engineer conditional positive (enforced S-phase entry, p27(Kip1)-antisense expression) or negative (G1-phase-specific growth arrest, p27(Kip1)-sense expression) growth control in mammalian cell lines and human primary cells.

RESULTS

The transgene control performance of all adenoviral expression configurations has been rigorously optimized for tight, balanced and maximum expression levels and was validated for intracellular as well as for secreted product in a variety of biotechnologically relevant cell lines (Chinese hamster ovary cells [CHO-K1], baby hamster kidney cells [BHK-21]) as well as in human cell lines (human fibrosarcoma cells [HT-1080]) and primary cells (human aortic fibroblasts [HAFs]).

CONCLUSIONS

We believe that multiregulated multigene-controlled adenoviruses are important assets for successful therapeutic reprogramming of mammalian cells in clinically relevant scenarios.

Design and in vivo characterization of self-inactivating human and non-human lentiviral expression vectors engineered for streptogramin-adjustable transgene expression

Adjustable transgene expression is considered key for next-generation molecular interventions in gene therapy scenarios, therapeutic reprogramming of clinical cell phenotypes for tissue engineering and sophisticated gene-function analyses in the post-genomic era. We have designed a portfolio of latest generation self-inactivating human (HIV-derived) and non-human (EIAV-based) lentiviral expression vectors engineered for streptogramin-adjustable expression of reporter (AmyS(DeltaS), EYFP, SAMY, SEAP), differentiation-modulating (human C/EBP-alpha) and therapeutic (human VEGF) transgenes in a variety of rodent (CHO-K1, C2C12) and human cell lines (HT-1080, K-562), human and mouse primary cells (NHDF, PBMC, CD4+) as well as chicken embryos. Lentiviral design concepts include (i) binary systems harboring constitutive streptogramin-dependent transactivator (PIT) and PIT-responsive transgene expression units on separate lentivectors; (ii) streptogramin-responsive promoters (P(PIR8)) placed 5' of desired transgenes; (iii) within modified enhancer-free 3'-long terminal repeats; and (iv) bidirectional autoregulated configurations providing streptogramin-responsive transgene expression in a lentiviral one-vector format. Rigorous quantitative analysis revealed HIV-based direct P(PIR)-transgene configurations to provide optimal regulation performance for (i) adjustable expression of intracellular and secreted product proteins, (ii) regulated differential differentiation of muscle precursor cell lines into adipocytes or osteoblasts and (iii) conditional vascularization fine-tuning in chicken embryos. Similar performance could be achieved by engineering streptogramin-responsive transgene expression into an autoregulated one-vector format. Powerful transduction systems equipped with adjustable transcription modulation options are expected to greatly advance sophisticated molecular interventions in clinically and/or biotechnologically relevant primary cells and cell lines.