Functional dissection of heterogeneity of responses to CAR T cells using Spatiotemporal Image-guided Genomic and Cellular Analysis (SaGA) in myeloma
Lawrence Boise
PhDEmory University
Project Term: October 1, 2023 - September 30, 2026
Despite remarkable progress in the last 20 years, multiple myeloma remains an incurable disease. In recent years, 2 CAR T cell products that target BCMA on the myeloma cell have been approved. These products result in remarkable initial responses however the duration of these responses has been disappointing. In this proposal, we will take a novel approach to isolate and characterize myeloma cells that interact with CAR T cells but are not killed by them as a potential resistance mechanism.
Multiple myeloma is a malignancy of the long-lived plasma cell of the bone marrow and while there has been incredible progress made in its treatment, it remains incurable. In the last 5 years this progress has included the FDA approval of several immunotherapeutic approaches including 2 CAR T cell products. Both CAR T cells target BCMA and while the overall rates and depth of responses have been remarkable, the duration of the responses have been somewhat disappointing with median time to progression of 12-15 months. Much focus has been on the loss of CAR T cell activity as the primary factor resulting in lack of long-term durability of responses. While this likely plays a significant role in the response, additional data indicate that mechanisms intrinsic to tumor cells such as loss of the BCMA target, may also contribute to resistance. However, given the depth of the responses, it is likely that resistant cells are relatively rare and heterogenous in nature. To uncover novel mechanisms of resistance we propose applying a functional assay that allows one to isolate single cells for further characterization. This method, called Spatiotemporal Image-guided Genomic and Cellular Analysis (SaGA) was initially developed to study phenotypic heterogeneity in collective migration of lung cancer cells. We have adapted this technology to precisely select and isolate myeloma cells that interact with CAR T cells, but are not killed by them. Once isolated, we will perform genomic analyses on these cells to determine how they differ from the general population of tumor cells. In the second aim we will validate the findings from our SaGA-based screen for resistant cells by testing the effects by inhibiting or activating the genes of interest through the use of CRISPR-based gene editing and/or gene over-expression and determining the effect on CAR T killing. We will also determine the role of these genes in myeloma outcomes through analysis of genomic datasets that are linked to clinical outcome as genes that are involved in cell-cell interactions may also influence myeloma cell interactions with cells that are present in the bone marrow that could influence the response to immune or non-immune-based therapies. We will also investigate expression of these genes in recently published data on gene expression changes associated with BCMA CAR T cell duration of response and of cells that are not initially killed by CAR T cells and found in the bone marrow one month after CAR T cell infusion. Finally, in the last aim we will test validated resistance genes in a mouse model. While determining factors within myeloma cells that can contribute to disease relapse in an area of intense investigation, this functional approach will be able to identify novel mediators of resistance that are not detectable using standard approaches.