Cooperative CAR targeting to selectively eliminate AML and minimize escape

Abstract

Acute myeloid leukemia (AML) poses a singular challenge for chimeric antigen receptor (CAR) therapy owing to its phenotypic heterogeneity and similarity to normal hematopoietic stem/progenitor cells (HSPCs). Here we expound a CAR strategy intended to efficiently target AML while minimizing HSPC toxicity. Quantification of target expression in relapsed/refractory patient samples and normal HSPCs reveals a therapeutic window for gated co-targeting of ADGRE2 and CLEC12A: We combine an attenuated ADGRE2-CAR with a CLEC12A-chimeric costimulatory receptor (ADCLEC.syn1) to preferentially engage ADGRE2^posCLEC12A^pos leukemic stem cells over ADGRE2^lowCLEC12A^neg normal HSPCs. ADCLEC.syn1 prevents antigen escape in AML xenograft models, outperforms the ADGRE2-CAR alone and eradicates AML despite proximate myelopoiesis in humanized mice. Off-target HSPC toxicity is similar to that of a CD19-CAR and can be mitigated by reducing CAR T cell-derived interferon-γ. Overall, we demonstrate the ability of target density-adapted cooperative CAR targeting to selectively eliminate AML and potentially obviate the need for hematopoietic rescue.

Keywords: CAR T cell therapy; ICAHT; IF-BETTER gate; acute myeloid leukemia; chimeric antigen receptor; combinatorial targeting; cooperative CAR; hematotoxicity; off-target toxicity; on-target toxicity.

Figure 1.. Antigen distribution and density inform AML target selection

(A-F) Flow cytometric quantitative profiling of AML surface target antigens ADGRE2, CLEC12A, CD33 and CD123 on AML bulk or LSCs in a relapsed/refractory AML patient cohort (n=39, Figure S1) and on normal hematological cells in a healthy adult donor cohort (n=8). Each dot represents an individual patient/donor sample. (A-B) Target antigen distribution profiles on AML cells as measured by percentage positivity gating. Horizontal bars represent median percentage target positivity in total patient population. ADGRE2^pos∪CLEC12A^pos (A∪C) denotes union of ADGRE2 and CLEC12A positivity (positive for either one or both antigens), ADGRE2^pos∩CLEC12A^pos (A∩C) denotes intersection of ADGRE2 and CLEC12A positivity (positive for both antigens). (C-E) Target antigen density profiles on AML and normal hematological cells as measured by median absolute numbers of surface molecules/cell. Dashed lines indicate 3×10² molecules/cell and 1×10³ molecules/cell. (F) Heatmap summarizing target protein densities of ADGRE2, CLEC12A, CD33, CD123 and CD19 on normal bone marrow-derived hematological cell populations. Numbers within heatmap indicate median number of surface molecules/cell. Cell frequency of the respective population relative to total live bone marrow cells is represented by horizontal bars and numbers indicating median percentage from n=8 independent healthy donor samples. (G) Mean target gene expression in different normal cell types of non-hematological origin based on single-cell RNAseq dataset. (H) Schematic comparing single-targeting and combinatorial CAR designs (OR gate, AND gate, IF-BETTER gate) and their predicted killing (red filling) and sparing (blank filling) characteristics on tumor (T) and normal (N) cells depending on ADGRE2 and CLEC12A target densities. Axes indicate ADGRE2 and CLEC12A target densities from negative (left and bottom, respectively) to low (middle) and high (right and top, respectively). Also see Figure S1.

Figure 2.. A CLEC12A-CCR increases sensitivity of ADGRE2-CAR-1XX

(A) Schematic depicting ADCLEC.syn1 combinatorial receptor design. (B) SFG-gammaretroviral bicistronic vector map for ADCLEC.syn1 expression. (C) EL4 murine lymphoma cell line variants expressing either no target (black), ADGRE2 alone (green), CLEC12A alone (violet), or ADGRE2 and CLEC12A together (orange). (D) 48h in vitro assay to measure cytotoxic activity of ADCLEC.syn1 vs 19-28z1XX CAR T cells at different effector:target (E:T) ratios in co-culture with EL4 cell line variants providing either no target, ADGRE2 alone, CLEC12A alone or ADGRE2 and CLEC12A together. T cell activation is represented by CD25 median fluorescence intensity (MFI) on T cells. Cytotoxicity was determined via flow cytometric enumeration of target cells. Data are represented as mean ± SEM. p value was determined via unpaired t test. (E) MOLM13 AML cell line variants with low CLEC12A density (5×10² molecules/cell) and varying ADGRE2 antigen density: high/WT (1×10⁴), low (1×10³) and very-low (4×10²). (F) 18h in vitro assay to measure cytotoxic activity of ADCLEC.syn1 vs its single receptor components (ADGRE2–28z1XX CAR or CLEC12A-BB CCR) vs untransduced T cells (UTD) in MOLM13 variants modeling antigen escape. Data are represented as mean ± SEM. p values were determined via unpaired t test. (G) M13-A^low-C^high MOLM13 variant with low ADGRE2 (1×10³ molecules/cell) and high CLEC12A (2×10⁵). (H) AML burden (total flux) and Kaplan-Meier survival analysis of M13-A^low-C^high-bearing mice treated with 5×10⁵ CAR^pos T cells. (I) M13-A^very-low-C^high MOLM13 variant with very-low ADGRE2 (4×10² molecules/cell) and high CLEC12A (1×10⁵ molecules/cell). (J) AML burden (total flux) and Kaplan-Meier survival analysis of M13-A^very-low-C^high-bearing mice treated with 5×10⁵ CAR^pos T cells. Also see Figures S2, S3, S4.

Figure 3.. CCR engagement regulates cytolysis directed to low antigen density

(A,C,E,G) MOLM13 variants with modified ADGRE2 (high vs low) and CLEC12A (low vs KO) levels: M13-A^high-C^low, M13-A^high-C^KO, M13-A^low-C^low, M13-A^low-C^KO. Bivariate plots illustrate how the respective ADGRE2/CLEC12A antigen densities (absolute number of surface molecules/cell) compare to the analyzed AML patient cohort (n=39) and their AML bulk (brown) as well as LSC (red) populations. (B,D,F,H) AML burden (total flux) and Kaplan-Meier survival analysis of mice bearing MOLM13 variants treated with 5×10⁵ ADCLEC.syn1 T cells. (I) AML burden (total flux) in week 2 and week 3 post ADCLEC.syn1 T cell injection in mice bearing MOLM13 variants. Data are represented as individual measurements and geometric mean with geometric SD. p values were determined via unpaired t test. (J) Kaplan-Meier survival of mice bearing either M13-A^low-C^low or M13-A^low-C^KO. Also see Figure S4.

Figure 4.. Low-dose ADCLEC.syn1 efficiently ablates AML with effective recall responses

(A,C,E,G,I,K) AML cell lines with modified ADGRE2 and CLEC12A densities used for xenograft CAR studies. Bivariate plots illustrate how the respective ADGRE2/CLEC12A antigen densities (absolute numbers of surface molecules/cell) compare to the analyzed AML patient cohort (n=39) and their AML bulk (brown) as well as LSC (red) populations. (B,D,F,H) AML burden (total flux) and Kaplan-Meier survival analysis of mice bearing MOLM13 variants treated with 5×10⁵ (B,D,F) or 1×10⁶ (H) CAR/CCR^pos T cells, comparing ADCLEC.syn1 vs its single receptor components (ADGRE2–28z1XX CAR or CLEC12A-BB CCR) vs untransduced T cells (UTD). (J,L) AML burden (total flux) of mice bearing M13-A^high-C^low (J) or M13-A^high-C^high (L) treated with UTD or ADCLEC.syn1 T cells at the indicated dose (1–2.5×10⁵). Arrows indicate repeated MOLM13 re-challenges (dose 5×10⁵, on d66 and d73 post initial CAR T injection) with either the same MOLM13 variant as on d0 (left graphs) or an antigen escape control variant M13-A^very-low-C^low (right graphs) with minimal target levels (Figure S5B) expected to cause AML relapse. Also see Figure S5.

Figure 5.. ADCLEC.syn1 eliminates leukemic stem cells in heterogenous AML PDX models

Three relapsed/refractory AML PDX models (PDX#1 in A-E, PDX#2 in F-G, PDX#3 in H-I) were utilized to assess CAR T cell efficacy (PDX clinical annotations and target phenotype in Figure S6A-D). T cell expansion and AML PDX burden were serially monitored via flow cytometry of PB and are shown as normalized T cell and AML cell counts per 100ul PB. Survival is shown as Kaplan-Meier analysis. (A,F,H) ADGRE2/CLEC12A antigen densities (absolute number of surface molecules/cell) of PDX LSCs compared to the analyzed AML patient cohort (n=39) and their AML bulk (brown) as well as LSC (red) populations. (B) ADGRE2/CLEC12A compared to CD33 antigen densities (absolute number of surface molecules/cell) on PDX#1. (C) Schematic of PDX#1 experimental setup for results shown in D-E (D) Primary engraftment of PDX#1 in NSG mice on d-11 was followed by treatment with 5×10⁵ CAR/CCR^pos T cells on d0, comparing UTD vs a reference CD33-CAR (33–28z1XX) vs ADCLEC.syn1. Mice receiving the reference CD33-CAR relapsed, and their bone marrow was harvested on d29 for subsequent secondary engraftment in NSG mice on d-16. (E) PDX#1 post-33–28z1XX failure was secondarily engrafted in NSG mice on d-16 and was followed by treatment with 2.5×10⁵ CAR/CCR^pos T cells on d0. (G) Engraftment of PDX#2 in NSG-SGM3 mice on d-9 was followed by treatment with 5×10⁵ CAR/CCR^pos T cells on d0. (I) Engraftment of PDX#3 in NSG-SGM3 mice on d-18 was followed by treatment with 5×10⁵ CAR/CCR^pos T cells on d0. Also see Figure S6.

Figure 6.. Humanized AML mouse model to assess ADCLEC.syn1 efficacy and HSPC toxicity

Humanized AML xenograft mouse model to assess CAR T cell hematotoxicity in the context of an in vivo anti-leukemic CAR T cell response. Anti-leukemic response and impact on normal human hematopoiesis was assessed upon receiving either no treatment or treatment with a reference CD19-CAR (19–28z1XX) vs ADCLEC.syn1. (A) Schematic of humanized AML xenograft CAR T cell hematotoxicity model. NSG mice were humanized via sublethal irradiation and injection of G-CSF-mobilized healthy donor-derived CD34^pos cells on d-21, followed by MOLM13-CD19^pos cell line injection on d-3, either untreated or treated with 2.5×10⁵ CAR/CCR^pos T cells on d0. (B) AML burden (total flux) of humanized mice bearing MOLM13-CD19^pos AML. (C-F) Representative ex vivo bone marrow distribution of AML and normal human hematopoietic cells on d7. (C) MOLM13-CD19^pos AML cells identified via positivity for CD33 and CD19 within total human CD45^pos cells (D) CD19^pos normal B cells and CD3^pos adoptively transferred CAR T cells within total human CD45^pos cells (excluding CD33^pos/CD19^pos MOLM13) (E) CD14^pos/CD16^neg normal classical monocytes within CD3^neg/CD19^neg human CD45^pos cells (F) CD34^pos normal HSPCs within lineage-negative (CD3^neg/CD19^neg/CD14^neg/CD16^neg) human CD45^pos cells (G) D7 ex vivo quantification of human bone marrow populations, with n=4–5 mice per group. Data are shown as individual counts and geometric mean with geometric SD. p values were determined via Mann-Whitney test.

Figure 7.. Off-target hematotoxicity is mitigated by reducing CAR T cell-derived IFN-γ

(A) In vitro assay to evaluate off-target HSPC toxicity due to soluble factors released upon CAR T cells engaging target cells. ADCLEC.syn1 CAR T cells with or without IFNG CRISPR/Cas9 editing were co-cultured with MOLM13-WT AML cell line for 10h at E:T ratio 1:1. Subsequently, cell-free supernatant (conditioned medium from CAR-T + AML-co-culture and individual controls) was collected and added to a separate in vitro culture of normal human CD34^pos/CD38^neg HSPC, with or without anti-IFN-γ blocking antibody. After 24h, HSPC phenotype (CD34/CD38 expression) and cell counts were measured via flow cytometry. (B) Absolute cell count and relative distribution of HSPC subsets upon in vitro culture with different CAR T + AML-conditioned media. Horizontal and error bars represent mean value and SD of technical triplicates. p values were determined via unpaired t test. FACS plots show representative CD34/CD38 HSPC phenotypes at time of assay read-out. (C) Schematic of in vivo model of CAR T cell IFN-γ-mediated off-target hematotoxicity. NSG mice were humanized via sublethal irradiation and injection of G-CSF-mobilized healthy donor-derived CD34^pos cells on d-21 (dose 6.0×10⁵), followed by injection of 19–28z1XX or ADCLEC.syn1 CAR T cells derived from the same donor (dose 3.0×10⁵ CAR/CCR^pos T cells, ± IFNG editing) on d0. (D) IFNG editing of 19–28z1XX and ADCLEC.syn1 T cells for in vivo study was demonstrated by intracellular IFN-γ staining 10h after in vitro culture with or without MOLM13-CD19^pos target cells at E:T ratio 1:1. (E) D7 ex vivo quantification of human bone marrow populations (lineage-negative CD34^pos/CD38^neg HSPCs, CD19^pos B cells and CD3^pos CAR T cells), with n=5 mice per group. Data are shown as individual counts and geometric mean with geometric SD. p values were determined via Mann-Whitney test. Also see Figure S7.

Figure 8.. ADCLEC.syn1 enhances distinction between AML and normal cells based on combined target signatures

(A) Chimeric receptor architecture of single CAR (ADGRE2-CAR) vs IF-BETTER gated CAR+CCR (ADCLEC.syn1). (B) Schematic outlining CAR T cell activity depending on target densities on AML and normal cells: ADGRE2-CAR kills only ADGRE2^high AML cells but fails to kill ADGRE2^low AML cells; ADCLEC.syn1 kills both ADGRE2^high and ADGRE2^low/CLEC12A^pos AML cells while sparing ADGRE2^low/CLEC12A^neg normal cells (C) Summary of in vivo activity of ADGRE2–28z1XX-CAR vs ADCLEC.syn1 against AML cell lines or PDX with target antigen densities as shown. Dashed line delineates in vivo target cell killing vs sparing as observed in experiments shown in Figures 2–5. (D) Projection of line for ADGRE2/CLEC12A in vivo killing threshold onto primary AML target phenotypes from r/r AML patient cohort. (E) Projection of line for ADGRE2/CLEC12A in vivo killing threshold onto normal hematopoietic cells