Designing Synthetic Gene Promoters for Gene Therapy Success
Synthetic promoters are a key driver of enhanced gene therapy precision and control.
In gene therapy, promoters act as vital “on/off” switches, dictating whether a therapeutic gene is active and to what extent. While delivery vehicles such as adeno-associated viruses (AAVs) can bring the therapeutic cargo to its intended destination, promoters can provide an additional layer of specificity and safety by restricting gene expression to particular cell types or tissues and by controlling the level of gene expression.
Often, strong ubiquitous natural promoters suffer from low expression specificity and can provoke adverse immune responses, while natural tissue-specific promoters typically display low activity. The development of new synthetic gene promoters designed for the precise control of transgene expression has the potential to enhance the safety and efficacy of gene therapies in line with evolving regulatory expectations.
SynGenSys has developed a transcriptional analysis and expression design platform, which utilizes bioinformatics analysis, data modeling, sequence design and testing modules to engineer high-performance synthetic promoters tailored to specific therapeutic goals.
Technology Networks spoke with Dr. David James, professor of bioprocess engineering at the University of Sheffield and co-founder and chief scientific officer at SynGenSys, to learn more about the importance of synthetic promoter design and SynGenSys’ latest promoter library tailored for natural killer (NK) cell therapies.
What distinguishes your design approach from more conventional gene promoter discovery methods, and how does this translate into practical advantages for drug discovery teams?
David James, PhD (DJ):
Promoter discovery usually relies on low- or high-throughput screening of natural sequences. Apart from the limitations inherent in using those sequences, this approach can be time consuming and unpredictable.
SynGenSys takes a bottom-up, computational approach. We mine transcriptional landscapes of both on- and off-target tissues to identify functional motifs and assemble promoters in silico with defined properties. This means drug developers can specify the therapeutic context, tissue or cell type for on- and off-target expression levels, right from the start.
Years of development of our platform have resulted in faster design cycles and fewer experimental iterations to generate synthetic promoters that are fit for purpose rather than adapted from generic viral or endogenous sequences.
BF:
DJ:
We design in functionality from the ground up, rather than conduct “black box” screening. Our platform enables this by using comparative mining of large genomic datasets to extract modular genetic building blocks, allowing us to construct promoters with defined activity profiles.
The combination of computational design with empirical validation makes production outcomes more predictable. However, all biological systems and processes are hypervariable, which means that a promoter that works well in one context may not necessarily be the best solution in another. Therefore, a “one-size-fits-all” solution, such as the widely used cytomegalovirus promoter, is becoming an outdated concept, particularly for modern, complex biologics, which may, for example, require coordinated stoichiometric balanced co-expression of multiple polypeptides.
We aim to create products that are easy to incorporate into existing workflows and minimize the risk of low or no product expression.
BF:
DJ:
This project had a clearly defined challenge: the promoters needed to be highly active in NK cells with very low activity in B lymphocytes. Additionally, we engineered out activity in human embryonic kidney cells to facilitate the use of any transgene that might otherwise be toxic to the host cell during lentivirus or AAV vector production. We addressed this by computationally comparing NK and B cell transcriptional landscapes to identify motifs unique to NK biology.
The result, our NK.SET™ library, delivers strong NK-specific expression with minimal off-target activity, enabling developers to design safer, more efficient NK-based immunotherapies. These promoters can be used off-the-shelf or easily tailored to specific customer needs. This success also sets the stage for similar libraries for T cells, tailored for both in vivo and ex vivo applications.
BF:
DJ:
We are the provider of a key enabling technology. The promoter is an integral part of a gene therapeutic payload, critical to its safety and efficacy.
Arguably, all gene therapies should utilize genetic elements specifically designed to be context-specific and fit for purpose.
It is important that genetic vector design occurs at the earliest stage of gene therapy development and that safety and efficacy are embedded into the biomedicine. Unlike small molecule therapeutics, the transgene promoter impacts both the biodistribution and pharmacodynamics of the medicine.
BF:
DJ:
We are moving towards very rapid in silico design of synthetic promoters that have a highly predictable bioactivity in vivo. An important underpinning technology will be computational systems that permit the user to define the properties of promoters and other components across a broad spectrum of potential applications.
In a gene therapy context, it’s incredibly important that patients receive medicines designed for maximal on-target specificity and efficacy with the lowest possible chance of adverse side effects. Similarly, with patients in mind, synthetic genetic systems have a core role in accelerating next-generation biopharmaceuticals to the clinic.
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