Cell-Based Medicine

While engineered immune cells have mostly been used to treat cancers, we are now seeing their incredible potential in autoimmune diseases such as lupus. This is a pivotal shift from immunosuppressive therapies to more precise, cell-based strategies that offer hope for durable remission and improved quality of life for patients refractory to current treatment options. 

Prior research has shown that control of autoimmune diseases is correlated with deep B-cell depletion, but current treatments do not fully eliminate circulating B-cells, particularly within the tissues¹. CAR-T cells are a promising option in this case due to their high-affinity specific target binding, ability to infiltrate, expand and survive in the tissues and established efficacy against malignant B-cells with multiple FDA approvals².

CD-19 directed CAR-T cells were used for the first time in 2021 in the treatment of a 20-year old woman with severe, treatment-refractory SLE. The infusion was well tolerated by the patient and delivered complete clinical remission after 3 months, with successful discontinuation of immunosuppressive agents without signs of disease up to 18 months³. Additional studies in patients with SLE showed similar promising results, with rapid cessation of clinical manifestations and stable production of CD19 CAR-T cells⁴. 

Importantly, no long-term B-cell aplasia was observed as B cells reconstituted around 100 days after the infusion. B-cell recurrence after CAR-T cell therapy was not associated with disease recurrence, which contrasts with treatment with conventional agents such as rituximab, which saw B-cell recurrence correspond with flares of SLE.

CAR-T therapy has already delivered life-changing results for patients with blood cancers. Despite the early success, there is room for new receptor designs—to improve performance and to expand into solid tumor treatment.

A new study from leading labs at Stanford University and the Parker Institute demonstrated meaningful advances in the ability to encode boolean logic into CAR-T cell receptors.¹

The first generation of chimeric antigen receptors have a fairly simple design. They consist of an antibody receptor—primarily targeting CD19 to-date—and the intracellular CD3ζ domain of a T-cell receptor.²

While this design achieves antigen targeting and T-cell activation, what if we could also encode logic that dictates specifically when cells are activated?

This study surveyed a wide range of new intracellular receptor components to achieve this. One example is a new design with two receptors that only activates when bound to CD19 AND HER2. Additionally, a different set of intracellular domains is used that circumvents the upstream signaling required by the CD3ζ domain.

The designs tested in this study showed impressive performance relative to previous attempts at logic-cated T-cell therapies in the literature.

So far, engineered T-cell therapies have made one change: the addition of a new receptor.

A clear North Star for the field of cell-based medicine is to expand the complexity and scope of cellular designs. Testing more complicated designs is a hard problem.

This new study introduces a modular screening platform to test a massive number of genetic knock-in (KI) sequences to program new functions.

Testing the function of large sets of synthetic DNA sequences in cells—especially in combination—is a challenging genetic engineering problem. It’s difficult to systematically add many different DNA regulatory elements or new surface receptors in a single experiment and keep track of what each sequence is doing to the cells.

This is where the beauty of DNA barcoding comes in. By labeling a library of sequences with short nucleic acid identifiers, it’s possible to conduct large screens in a pooled fashion, where all of the results are read out at once—and then separated in analysis using the barcodes.

With this clever genetic engineering approach, the authors were able to screen a library of ~10,000 new DNA designs in different T-cell therapies. This study focused on new elements that helped T-cells avoid exhaustion, which is one of the major limitations of current medicines in the clinic.

This screening platform should be broadly useful for cell programming.

T-cell therapy is complex. A patient’s cells are removed from their body, engineered, and then reintroduced. Much of the field’s current focus is on streamlining this process and improving the engineering step.

But what if the future of cell therapy looked totally different?

A study from Stanford University engineered microbes on the skin to trigger a cancer-killing response from T-cells.

CAR-T therapy is an autologous treatment, meaning that the final medical product consists of a patient’s own cells. This is a powerful new paradigm, but introduces considerable logistical complexity into the treatment process. A patient’s T-cells are isolated, transformed with genetic engineering, and then returned to the blood.¹

Many labs and companies are developing engineering solutions to simplify this process, making it faster and more affordable.

But what if there are entirely different avenues for programming T-cells to attack cancer cells?

A study from Stanford University demonstrated one possible alternative. Researchers engineered microbes naturally present on the skin to express cancer antigens on their surface. Remarkably, T-cells sampled these antigens and migrated to attack and kill cancer cells.

Imagine a future where T-cell therapy is as simple as applying a lotion to your skin.

The first immune cells engineered with chimeric antigen receptors (CARs) were T-cells. In the next generation of approaches, researchers have experimented with other immune cell types, including macrophages.

In this study, CAR macrophages with more sophisticated receptors showed substantial improvements over the first generation of this therapy.

This work describes the development of second-generation CAR macrophages derived from induced pluripotent stem cells. These cells have been engineered with enhanced capabilities to target and kill cancer cells, thanks to a dual signaling system that combines a traditional CD3ζ with a toll-like receptor domain.

This design allows the macrophages to better recognize and eliminate tumor cells, resist alternative activation, and manipulate the tumor environment effectively. The results demonstrate significantly improved anti-tumor functions compared to earlier versions, suggesting potential for more effective use of additional immune cells beyond T-cells.

The early antigen target of CAR-T cells for blood cancers was CD19. CD19 is a universal marker of B-cells, which are capable of completing regenerating after being eliminated during a course of CAR-T therapy.

An open question for the next generation of CAR-T therapies has been what additional targets will be viable beyond CD19. In new clinical results in glioma patients, CAR-T cells targeting GD2, which is highly expressed in a subset of cancers, the field saw early signs of promise for a novel target with sufficient specificity and safety.

This study describes the results of a Phase I clinical trial using GD2-CAR T cell therapy for treating diffuse midline gliomas with H3K27M mutation, a challenging type of brain cancer in children and young adults. The therapy involves engineering T cells to target GD2, a molecule highly expressed on these tumor cells.

Results showed that some patients experienced significant clinical and radiographic improvements with manageable side effects related to inflammation. These findings suggest potential for CAR-T therapy in treating a solid tumor with a novel genetically informed antigen target for the receptor.

While it’s still early days for the field, one thing is clear: cell-based therapies are here to stay. Between microbes, stem cells, and immune cells, we are likely only scratching the surface of what is possible.¹

As we’ve covered in this report, researchers are hard at work building more sophisticated cellular designs. We are learning how to bake boolean logic into cell circuits, and how to test new designs at a massive scale using the powerful read/write/edit tools of modern synthetic biology.

Beyond cellular design, the future of cellular delivery could also look completely different.² Many labs and companies are developing new solutions for dramatically improved ex vivo cell therapy, and a new wave of in vivo approaches—ranging from mRNA programming to engineered skin microbes—are right around the corner.

As these new technologies make their way into the clinic, we expect that cell-based therapies will expand across blood and solid cancers, autoimmune indications, and beyond.

While an incredible option for patients, the realities of CAR-T accessibility, manufacturing and cost forces us to consider the question: is it possible to overcome the many barriers that prevent widespread use of this treatment?

Only by acknowledging the many deficiencies can we start to build a network of solutions that ultimately bring life-saving drugs to more patients

Anti-BCMA CAR-T therapies have achieved impressive clinical outcomes in relapsed or refractory multiple myeloma (r/r MM), but there are several challenges that limit accessibility. 

The current personalized manufacturing process for commercial CAR-T products takes 3-4 weeks and is extremely expensive. Patients suffering from rapid disease progression sometimes cannot afford to wait this long for treatment. Additionally, this therapy is typically delivered in an inpatient setting at a large academic medical center [1], which creates geographical & cost barriers to access.

To address these challenges, several novel approaches are being tried:

• Bridging therapies to limit progression while treatments are prepped
• Rapid manufacturing platforms such as FasT CAR-T cells, which can be produced in 24 hours [2]
• Allogeneic (“off-the-shelf”) therapies
• Utilizing non-viral transfection
• Initiating treatment earlier for high-risk patients

The number of companies pursuing cell therapy has exploded the past few years, but most are still relying on entirely bespoke processes for small batch early-stage trials. As the industry progresses towards the pivotal & commercial stage, there is a clear need to develop robust & scalable manufacturing processes to alleviate supply bottlenecks and bring down costs.

• CGT has produced a novel manufacturing approach that still closely mirrors academic research (open handling, manual labor, inefficient equipment use), all contributing to costs >$100K per treatment
• Autologous therapies are inherently limited to one unit batches and this is still the dominant approach
• Patients are generally late-line and thus the variability in the quality of starting material is a big challenge to producing a final product on the other end of the process
• Researchers and companies are addressing these limitations with a variety of approaches, including single cell processing devices, decentralized manufacturing, non-viral gene transfer methods, novel QC testing methods and allogeneic therapies