Why promoter design is no longer just an expression checkbox, it’s the key to therapeutic endurance.
As the cell and gene therapy (CGT) space matures and commoditizes, many low-hanging fruits have been picked. We are now facing another frontier in biology: getting a gene into a cell is one thing; getting it to express correctly over time is another. At Annogen, we are seeing a shift in focus (in attention) from delivery vehicles to expression control. Specifically, our partners in biopharma are hitting three critical bottlenecks that standard promoters (like viral CMV or mammalian housekeeping PGK) simply cannot solve. 1. Tissue Specificity (The “Off-Target” Problem)Cell-type–specific gene delivery has improved substantially, but remains imperfect, resulting in transduction of both on-target and off-target cells. In this context, commonly used (viral) promoters lack intrinsic specificity and drive expression across all transduced cell types. As a consequence, therapeutic gene expression is not fully restricted to the intended tissue, leaving off-target activity and associated safety risks a substantial concern. Incorporating cell-type–specific promoters offers a solution by further confining expression to the desired cellular context, thereby improving precision and reducing potential toxicity.and housekeeping.
2. Cellular Exhaustion (The “Always-On” Problem)In CAR-T therapies, tonic signaling, where the CAR is constantly activated, can lead to T-cell exhaustion before the patient is even treated and the expression level of the CAR can be critical factor in this. Therapy developers are therefore exploring “smart” promoters that are inducible or autoregulated, finetuning the response to the moment the therapeutic action is required.
This is perhaps the most frustrating hurdle, mostly encountered with ‘foreign’ viral sequences which can be quickly recognized as foreign and silenced but it can also occur with endogenous human promoters that do not show enough autonomy to remain active irrespective of their integration site. The result: A therapy might work perfectly in vitro, but in vivo, the cell’s epigenetic machinery shuts down expression.
At Annogen we use the SuRE™ (Survey of Regulatory Elements) platform to tackle these issues and commoditize promoter customization. Instead of testing a handful of known or designed promoter elements, we functionally screen millions of non-coding DNA fragments in parallel in the relevant model systems. Using machine learning approaches, we iteratively refine promoter designs, relying on our unique capability for large scale testing in the relevant (in-vivo) model systems to come to validated promoter designs. This approach experimentally identifies unique, non-viral promoters that are resistant to silencing and can be tissue-specific or condition-specific, for example driving expression in response to tumor-environment or the presence of a particular drug. This way, we don’t just find a good-enough promoter; we find your promoter.
