Affinity Matured CD72 CAR-T Improves Efficacy Versus Low Antigen Density B-Cell Non-Hodgkin Lymphoma Models

Background:

Even in the CD19 CAR-T era, many patients with relapsed/refractory B cell non-Hodgkin lymphoma (B-NHL) need additional therapeutic options. Our group has identified CD72 as a therapeutic target for high-risk B-cell malignancies and validated anti-CD72 CAR-Ts (“nanoCAR”s) for these indications in relevant preclinical models (Nix et al., Cancer Discovery 2021, Temple et al., ASH 2022). However, patient B-NHL tumors may express a wide distribution of surface CD72, and our current CAR-T designs may be less efficacious for tumors with low antigen density.

We previously described the development of affinity-matured binders extending from our initial published anti-CD72 nanobody clone (NbD4), with ~20-60x higher target affinity (Temple et al.). Here, we tested the hypothesis that these higher affinity binders would better eliminate low antigen density B-NHL models, both in vitro and in vivo, and impact other properties including avidity, and antigen binding epitopes.

Methods:

Anti-CD72 affinity-matured binders were developed by random mutagenesis of CDR regions of the nanobody clone NbD4 (described in Temple et al.). CAR-T cells were generated by lentiviral transduction. CAR-T cell efficacy was tested by in vitro cytotoxicity assays and Incucyte live-cell imaging against lymphoma cell lines. For in vivo studies, JeKo-1 tumor cells were implanted at 1e6 per mouse and then mice were treated with 3.5e6 CAR+ T-cells at day 7. Tumors from mice bearing JeKo-1 that relapsed on CAR-T treatment were isolated and used in Incucyte assays.

Results:

We analyzed publicly available datasets of patient cohorts and found that CD72 is widely expressed, though with a broad distribution, across diffuse large B cell lymphoma (DLBCL), follicular lymphoma, and Burkitt lymphoma patient samples. In both DLBCL and chronic lymphocytic leukemia (CLL), high expression of CD72 correlated with significantly shorter overall survival (DLBCL: GSE10846, n=233, p = 0.0382; CLL: GSE22762, n=107, p = 0.00124, log-rank test). We confirmed expression of CD72 on 8 lymphoma cell lines by flow cytometry. In vitro against a subset of these lines, affinity-matured clone NbD4.13 showed improved cytotoxicity compared to parental NbD4 and similar cytotoxicity to a humanized variant (H24 clone).

We developed a JeKo-1 model of low CD72 antigen density (4.7x MFI reduction) by CRISPR/Cas9 knockout of endogenous CD72 and re-expression of a recombinant construct. In this “CD72 low” model, affinity matured clone NbD4.13 led to improved cytotoxicity vs. H24 (p = 5.1e-4 by t-test). We previously showed that tumor isolated from JeKo-1 mice treated with H24 CAR appear to have reduced antigen expression at relapse (Temple et al.). We cocultured these post-relapse JeKo-1 tumors with various CD72 nanoCARs and found that NbD4.13 eliminates tumor significantly faster at 24 hours than H24 by live-cell imaging (p = 0.0054 by t-test). In vivo in a JeKo-1 model, NbD4.13 also out-performed the H24 clone with respect to survival benefit (p = 0.011 by log-rank for survival) (Fig. 1).

To assess if additional differences beyond affinity may determine the efficacy of NbD4.13, we performed structural modeling using AlphaFold and HADDOCK. However, this analysis predicts NbD4, NbD4.13 and H24 bind a similar non-linear epitope on the CD72 monomer. Furthermore, acoustic force microscopy did not reveal a significant difference in binding avidity for any of the compared CD72 nanoCAR constructs.

Finally, we evaluated whether it could be possible to pharmacologically increase CD72, as co-treatment strategy to enhance efficacy of CD72 nanoCARs. We found that the Protein Kinase C inhibitor Bryostatin-1, previously demonstrated to increase CD22 antigen density (Ramakrishna et al., Clin Cancer Res 2019), could also significantly increase surface CD72 in vitro in both B-ALL and B-NHL models (Fig. 2).

Conclusion:

NbD4.13-based anti-CD72 CAR is a promising candidate for further preclinical development for treatment of relapsed/refractory B-cell non-Hodgkin lymphoma. Given anticipated heterogeneity in CD72 expression in various lymphomas, pharmacologic co-treatment strategies may be considered to modulate tumor antigen density.