Next-generation genetic engineering of the pan-leukocyte antigen CD45 to facilitate CAR-T cell therapy against hematologic malignancies

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SUMMARY/ABSTRACT (PROJECT 2): Next-generation genetic engineering of the pan-leukocyte antigen CD45 to facilitate CAR-T cell therapy against hematologic malignancies Currently, chimeric antigen receptor (CAR)-T cells must be individually designed for each disease, targeting lineage-associated antigens such as CD19 for B-cell malignancies or BCMA for myeloma. While this approach has led to the successful treatment of hundreds of patients on clinical trials or with commercial CAR-T cell therapies, from a drug development standpoint this approach is inefficient. By targeting a pan-hematologic antigen, a single “drug” could be used for all indications, thereby accelerating clinical research. CD45 is a receptor tyrosine phosphatase that is expressed on the surface of most hematopoietic cells, from immature stem cells to differentiated progeny. As expected, antibody-drug conjugates targeting CD45 cause profound myeloablation and are in clinical development as conditioning agents prior to stem cell transplantation. A unique hurdle limiting the use of anti-CD45 CAR T cells (CART-45) is that T cells themselves express CD45, and CART- 45 are therefore vulnerable to fratricide. Furthermore, CD45 is crucial for proper function of the T cell immune synapse. The overarching goal of this project is to render CD45 targetable using genetic engineering of T cells and of hematopoietic stem cells (HSC). To achieve this goal, we will test the central hypothesis that site-specific mutation of CD45 in hematopoietic cells (including T cells) can abrogate recognition by CART-45 while retaining all other domains required for the function of this molecule. We expect that this approach will prevent T cell dysfunction and myeloablation. This will be accomplished in three specific aims. In Aim 1, we will generate fratricide-resistant CD45-targeting CAR-T cells. We have identified a candidate CAR construct based on unbiased functional screening and shown that CART-45 are indeed subject to fratricide. While this fratricide could be rescued by CRISPR-based knock out of CD45, CD45-deficient CART cells were dysfunctional. Using alanine mutagenesis, we then identified the target epitope on CD45 that is recognized by our lead CAR candidate and we have now successfully edited this epitope to abrogate fratricide, resulting in CAR-T cells that recognize native CD45 in trans without themselves being the target of anti-CD45 CAR. In this aim we will test the hypothesis that the function of CD45-edited T cells is equivalent to unmodified control T cells, and superior to that of CD45- deleted T cells. In Aim 2, we will genetically engineer hematopoietic stem cells to generate a CART-resistant hematopoietic system. To demonstrate that engineered CD34+ HSC’s are resistant to CD45 targeted CAR-T cell therapy, engineered HSPC’s will be engrafted into immunodeficient mice followed by treatment with CD45 CAR-T cells. Finally, to target CD45 in human AML we will disrupt CD45 expression in primary human AML and test leukemogenicity in vitro and in vivo. In Aim 3 up to 6 patients will undergo allogeneic stem cell transplantation using donor stem cells where CD45 expression has been edited using CRISPR/Cas9, followed by infusion of donor-derived CART-45. Successful completion of this Aim will provide proof-of-concept for our overall strategy to create a leukemia-specific antigen using gene editing tools.