Forging a New Path for Durable and Effective Immunotherapies with Functional Proteomics

Drug development is a complex process with many steps that a drug candidate must go through, from early-stage R&D to FDA approval and commercialization; moreover, many drug candidates never make it to human trials. The development of safe and effective immunotherapies is especially challenging due to the complexity of the immune system. Elucidating the mechanisms and pathways that regulate the immune system’s response has enabled great strides in transforming the immunotherapy landscape, but there are still hurdles to overcome. Cutting-edge proteomics can help to confirm the function of immunotherapies to improve the safety, efficacy, and long-term durability of novel therapies.

IsoPlexis’ functional single-cell and bulk proteomics overcome challenges of the immune system by enabling researchers to characterize immune cell function and immunotherapy candidate choice with deeper access to in vivo biology. With functional proteomics, it’s possible to fine-tune immunotherapy candidates as well as identify differentiators of immune cell potency, cell product toxicity, and functional differences between responsive and nonresponsive patients. Because immune cells have a wide range of functions, characterizing each individual cell is critical. Polyfunctional cells, those that secrete multiple cytokines simultaneously, are the “superhuman” cells of the body, driving key processes and often correlating with improved outcomes such as therapeutic response, efficacy, and persistence. IsoPlexis’ platform has the unique ability to identify and analyze these superhuman polyfunctional cell subsets, revealing critical functional cellular attributes that can help optimize cell therapies and improve manufacturing methods.

Optimizing Cell Therapies with Functional Proteomics

Chimeric antigen receptor (CAR)-T cells have shown promise for treating certain B-cell malignancies, including relapsed/refractory multiple myeloma (MM). Targeting the B-cell maturation antigen (BCMA) has produced favorable results for CAR-T therapy of MM so far, but relapse is a persistent problem for MM patients. Thus, there is a critical need for development of CAR-T therapies that drive improved outcomes for patients aimed at overcoming this challenging problem.

In a study published in Blood Advances, researchers created a new CAR capable of binding multiple antigens. Hypothesizing that a combinatorial approach may compensate for the downregulation of specific individual antigens by cancer cells, the group designed a custom receptor based on APRIL (a proliferation-inducing ligand) and transduced it into T cells to create APRIL CAR-T cells.

APRIL is the natural ligand of both BCMA and TACI (trans- membrane activator and CAML interactor), a member of the same superfamily as BCMA that is also abundant on most myeloma cells. Initial binding assays against soluble BCMA and TACI proteins showed that APRIL CAR-T cells bound to both ligands relatively weakly. In order to strengthen the interaction, the team created a trimeric APRIL-based binding domain (TriPRIL) by linking three truncated APRIL binding domain monomers together. TriPRIL CAR-T cells showed not only enhanced binding relative to APRIL CAR-Ts, but also activated more robustly when co-cultured with MM target cells.

Beyond the ability to detect and interact with cancer cells, CAR-T cells also need to be durable and adaptable in order to promote positive clinical outcomes. To assess durability, the team looked at how TriPRIL CAR-T cells proliferate and found responses similar to BCMA or APRIL CAR-T counterparts. To examine the proliferative capacity of these constructs, the authors then looked at polyfunctionality—the ability of an individual cell to secrete a range of cytokines simultaneously—using IsoPlexis’ single-cell functional proteomics.

Single cell polyfunctionality correlates with CAR-T products that induce clinical responses in lymphoma patients. TriPRIL CAR-T cells showed either comparable (CD4+) or highly elevated (CD8+) proportions of polyfunctional cells relative to BCMA and APRIL CAR-Ts and possessed the highest polyfunctional strength index (PSI) of the three CAR-T cell types examined. This provides an important insight into CAR durability and adaptability.

In another study published in Nature Communications, researchers utilized IsoPlexis’ single-cell proteomics to better understand the functional drivers of T cell persistence in response to a novel agonist in treating solid tumors. Mice treated with the novel agonist recruited the adoptively transferred cells into tumors, which were found to be highly polyfunctional and adept at simultaneously secreting both effector and chemoattractive cytokines. These superhero cells, identified by IsoPlexis’ technology, were predictive of  anti-tumor response. In a Phase 1 clinical trial for melanoma patients, the circulating NK cell response and clear mechanistic upregulation of these polyfunctional cell subsets were found to be highly persistent and sustained a longer anti-tumor response than traditional ACT treatment with IL-2.

These data suggest that polyfunctionality and functional phenotyping with IsoPlexis’ single-cell proteomics may provide a more comprehensive biomarker in solid tumor indications, accelerating insights in cancer immunology, and revealing predictive functional superhero cell subsets to advance the development of vaccines.

The Superhuman Cell Library Unlocks New Research Opportunities

Functionally profiling single cells is a critical step when developing immune therapies, as these cell subsets provide valuable insights into immune persistence, anti-tumor activity and protective immunity. Revealing the presence of these superhero or supervillain cells helps researchers create more robust therapies for improved clinical outcomes.

IsoPlexis’ functional phenotyping enables researchers to identify these “superhuman” polyfunctional cells, allowing them to optimize their immunotherapy candidates as well as identify what differentiates immune cell potency, persistence, and the functional differences between responsive and nonresponsive patients.

A library of these superhuman cells is now available through IsoPlexis’ Functional Cell Library: a free, comprehensive resource to advance and accelerate the development of effective therapeutics.


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