Surface Proteomics Reveals CD72 as a Target for In Vitro–Evolved Nanobody-Based CAR-T Cells in KMT2A/MLL1-Rearranged B-ALL

Abstract

Alternative strategies are needed for patients with B-cell malignancy relapsing after CD19-targeted immunotherapy. Here, cell surface proteomics revealed CD72 as an optimal target for poor-prognosis KMT2A/MLL1-rearranged (MLLr) B-cell acute lymphoblastic leukemia (B-ALL), which we further found to be expressed in other B-cell malignancies. Using a recently described, fully in vitro system, we selected synthetic CD72-specific nanobodies, incorporated them into chimeric antigen receptors (CAR), and demonstrated robust activity against B-cell malignancy models, including CD19 loss. Taking advantage of the role of CD72 in inhibiting B-cell receptor signaling, we found that SHIP1 inhibition increased CD72 surface density. We establish that CD72-nanobody CAR-T cells are a promising therapy for MLLr B-ALL. Significance: Patients with MLLr B-ALL have poor prognoses despite recent immunotherapy advances. Here, surface proteomics identifies CD72 as being enriched on MLLr B-ALL but also widely expressed across B-cell cancers. We show that a recently described, fully in vitro nanobody platform generates binders highly active in CAR-T cells and demonstrate its broad applicability for immunotherapy development. This article is highlighted in the In This Issue feature, p. 1861

Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia

“…4c . Interestingly, these were centered on the lymphoid marker CD72, which a proteomic screen recently implicated as a target in infant ALL 27 . Coexpression of nonphysiological combinations was measured by flow cytometry, where commercial antibodies existed, confirming that dual-targeting would encompass >90% of leukemic cells ( Fig.…”

Single cell mRNA signals reveal a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia

“…4C . Interestingly, these were centred around the lymphoid marker, CD72, that a proteomic screen recently implicated as a target in infant ALL 26 . As surface marker therapies evolve and enable the targeting of two antigens simultaneously, non-physiological co-expression of markers may represent an attractive therapeutic avenue.…”

Surfaceome Profiling of Rhabdomyosarcoma Reveals B7-H3 as a Mediator of Immune Evasion

“…As a result of the technological advances and reduced costs, conventional proteomics has become an attractive tool for target discovery and therapeutic development. However, it suffers from low sensitivity for cell surface proteins, which are significantly less abundant and soluble than cytosolic proteins [ 29 ]. Although surfaceomic approaches have been shown to circumvent this challenge and enhance target discovery, it has not been widely adopted, as several challenges have limited its use [ 30 , 31 , 32 ].…”