Value of Cellular Proteomics: Confirming Critical Cellular Immune Function After Making Complex Gene Edits in Solid Tumor Therapies

In the previous installment of this series, we discussed how single-cell functional proteomics can increase confidence in therapeutic development by confirming correlative cell product function and potency. In this installment, we will discuss how this technology can also aid in discovering the impact of novel edits on each cell for use in cell therapies.

Current Development Challenges in Gene Editing Require Functional Confirmation

Immune monitoring is notably complex. We have previously discussed how legacy technologies are inadequate in fully assessing functional response and quality characteristics that encourage efficacy, potency, and safety, particularly when noting that the mechanism for both clinical effects and cytotoxicity can be heavily mediated by cytokines. IsoPlexis’ single-cell functional proteomics has the ability to capture the specific cytokines each cell secretes to provide the essential data needed to develop and optimize immunotherapies.

Illustrating the challenge: If you are evaluating the ability of a cell type for use in cell therapies, such as T cells or NK cells, and manipulating such cells with gene edits as well as various cell expansion steps, functional profiling is necessary to detect the cellular secretions that orchestrate the surrounding immune populations, as well as attack the tumor. IsoPlexis’ technology uniquely captures the full range of relevant cytokines from each immune cell, connecting each cell to the many secreted cytokines that coordinate the immune system.

Three Applications to Gene Edited and Allogeneic Cell Therapy in Solid Tumor Contexts, as Illustrated in GEN News

Autologous cell therapy development faces several challenges, such as insufficient source material quality or quantity, leading to a delay in patient treatment. Unlocking the potential of allogeneic cell therapies may help to overcome the current challenges of autologous cell therapies. In order to make the leap from autologous to allogeneic, confirming the function of gene edited cell therapy products will be critical, as the product will be “off the shelf.” This is where IsoPlexis’ ability to uniquely identify the functional changes due to gene edits will help accelerate gene edited therapy development.

Precision Biosciences is one of the companies leading the charge on allogeneic cell therapy development. Their next generation genome editing platform, ARCUS, is a homing endonuclease-derived genome editing platform that leverages the small size and high specificity of a natural genome editing system. In an interview with the Scientist, Vladimir Senyukov, Director of BioAnalytical Development at Precision Biosciences, discusses how single-cell functional proteomics informs the development and manufacturing of gene-edited allogeneic CAR-T cell products.

• Coupling single-cell proteomics translational information in gene edited cell therapy, with SC genomics discovery information:
  “My current project involves using IsoPlexis to profile the cytokine signatures of polyfunctional cells that we might have in a cell population,” said Senyukov. “Then we take those cells and employ a single cell RNA sequencing approach where we can also try to identify that polyfunctional cytokine signature in the RNAseq data. From there, we can try to identify what else—what other genes are associated with that signature—and then try to find the next genotype or other properties of a cell that makes them unique or different or better.”
• Verifying each edited CAR-T cell for all cellular functional impacts, post edit:
  Single-cell functional proteomics is valuable here as well, explained Senyukov. “When optimizing, or when changing manufacturing processes to make better cells, it can be used to monitor cellular changes. It is especially valuable in screening for polyfunctionality, which is key, because based on the literature, polyfunctionality is one of the most important factors driving clinical efficiency.”
• What’s next in Gene Edited Cells that groups with the IsoLight are working on: Highly functional donors with Allogeneic Samples:
  Ultimately, Senyukov would like to break new ground for allogeneic CAR-T cells, given that most of the existing research on polyfunctional T cells comes from cases of autologous cell transfer. “There haven’t been too many studies on the importance of polyfunctionality for allogeneic material, and there’s a need to find specific signatures that could give us information about functional efficiency in a particular patient group. It’s also about trying to find other pathways of gene expression associated with polyfunctionality that could allow future optimization of manufacturing processes.”

Accessing These Highly Polyfunctional Cells & Determining PSI to Optimize Gene Edited & Allogeneic Therapeutic Potency

IsoPlexis’ Polyfunctional Strength Index, or PSI^TM, has helped to capture the potency of important and highly functional immune cell subsets, which have correlated to in vivo outcome. PSI is a powerful and unique metric, developed by IsoPlexis, with a wide range of applications in engineered immune cell therapy research and development.

In gene edited cell therapies, the metric is being used in pre-clinical discovery to understand correlations with in vivo response and confirm the ability to maintain potency and fitness, without undesired functional responses, post edits. This metric can also identify the most potent and effective cells, meaning that researchers are able to make informed decisions within the development of their cell therapy programs, rather than taking chances with unknown cellular function and delaying the advancement of their therapies.

When it comes to discovering leads to develop and advance next generation immunotherapies, IsoPlexis’ platforms provide the essential functional data needed to confidently characterize these therapies in product manufacturing and accelerating therapies to market, while other technologies are not able to provide this true functional response data which has proven correlative.

See exactly what your edited and engineered cells are doing and confidently make decisions in your cell therapy development pipeline. Ready to take the next step? We’d love to have a conversation.