NTLA5001, a T Cell Product Candidate with CRISPR-Based Targeted Insertion of a High-Avidity, Natural, WT1-Specific TCR, Shows Efficacy in In Vivo Models of AML and ALL
Authors: Ruggiero Eliana , Liu Dai , Prodeus Aaron , Becker Amy M , Foisey Maxwell , Balwani Ishina , Dutta Ivy , Zhang Qingzhan , Arredouani Simo M , McKee Mark , Ciceri Fabio , Sepp-Lorenzino Laura , Bonini Chiara , Schultes Birgit C 
Published: November 2020

Adoptive cell therapy using T cells expressing transgenic (tg) tumor antigen-targeting T cell receptors (TCRs) has become an attractive modality to treat hematological and solid cancers due to a broader array of accessible targets relative to CAR-T cell therapies. However, high-avidity TCRs specific for shared oncogenic antigens are difficult to identify. In addition, manufacturing of TCR-redirected T cells with single TCR specificity is desired to avoid mispairings and competition with endogenous chains, which can negatively impact T cell specificity and TCR expression levels. This can be achieved with CRISPR/Cas9-mediated replacement of the endogenous TCR α and β chains, by knocking out the TRAC and TRBC genes and inserting the tgTCR into the TRAC locus. While CRISPR/Cas9 genome editing has been demonstrated to be highly efficient, simultaneous edits in different loci could result in increased translocations, potentially impairing the quality and safety of the cell product. Moreover, existing cell engineering technology negatively impacts T cell quality and yield.
Here, we focused on engineering T cells with specificity for Wilms' Tumor 1 (WT1), a transcription factor overexpressed by a wide range of hematological and solid tumors, that has both, restricted expression on healthy tissues and a strong correlation with oncogenesis. By applying rapid isolation technologies of WT1-specific T cells from healthy donors, we identified a lead TCR to the WT137-45 epitope, restricted to the common human leukocyte antigen, HLA-A*02:01. T cells expressing this tgTCR showed nM avidity and killed leukemia cell lines and primary acute myeloid leukemia (AML) blasts at low effector-to-target cell ratios. Epitope specificity evaluation by alanine scanning suggested that the minimal peptide recognition sequence for this TCR is restricted to WT1. Further, the lead TCR was able to activate CD8+ and CD4+ T cells, which may be beneficial for T cell persistence.
By developing an improved T cell engineering process, we have achieved multiple sequential gene edits in primary human T cells, leading to knockout of the endogenous TCR with up to 99% efficiency and insertion of tgTCRs into 55-80% of the cells. This cell engineering process is scalable, adaptable to a closed system, and results in marked improvements in T cell expansion, yield, stem cell memory phenotype and T cell polyfunctionality, such as cytotoxicity, cytokine release and proliferation in response to WT1+ target cells. Additionally, the high viability profile of the process readily allows for sequential CRISPR/Cas9 gene knockout in T cells, leading to near-complete endogenous TCR removal while limiting TRAC/TRBC translocation to levels close to those found in untreated cells.
T cells engineered to express the lead TCR using this process resulted in potent anti-tumor activity in vivo. Disseminated primary AML patient derived xenograft and acute lymphoblastic leukemia (ALL) cell line models were established by intravenous injection of the tumor cells in NSG or NOG mice. Animals were treated subsequently with WT1-specific or control T cells. Almost complete tumor growth inhibition in the blood and bone marrow was noted in the primary AML model. In the fast growing ALL model, WT1-T cells significantly reduced tumor burden and increased survival compared to control groups, which could be further boosted in human IL-15-expressing NOG mice vs. standard NOG mice. No signs of graph-versus-host disease (GvHD) were observed during the course of the study, which is consistent with removal of the endogenous TCR. NTLA-5001 is being advanced into clinical development for AML immunotherapy. Given the expression of WT1 in many solid tumors, engineered WT1 TCR-T cells are being further explored in those indications.

Disclosures
Liu: Intellia Therapeutics: Current Employment. Prodeus:Intellia Therapeutics: Current Employment. Becker:Intellia Therapeutics: Current Employment. Foisey:Intellia Therapeutics: Current Employment. Balwani:Intellia Therapeutics: Current Employment. Dutta:Intellia Therapeutics: Current Employment. Zhang:Intellia Therapeutics: Current Employment. Arredouani:Intellia Therapeutics: Current Employment. McKee:Intellia Therapeutics: Current Employment. Ciceri:Intellia Therapeutics: Membership on an entity's Board of Directors or advisory committees. Sepp-Lorenzino:Intellia Therapeutics: Current Employment. Bonini:Kiadis: Membership on an entity's Board of Directors or advisory committees; Kite/Gilead: Membership on an entity's Board of Directors or advisory committees; Molmed: Membership on an entity's Board of Directors or advisory committees; Allogene: Membership on an entity's Board of Directors or advisory committees; Intellia Therapeutics: Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding. Schultes:Intellia Therapeutics: Current Employment, Current equity holder in publicly-traded company.