New research shows that engineering epitopes on donor hematopoietic stem and progenitor cells (HSPCs) used in bone marrow transplants can give hematopoietic lineages selective resistance to monoclonal antibodies or chimeric antigen receptor (CAR) T cells without changing protein regulation or function. This tactic makes targeting genes essential for leukemia survival possible, even if those genes are also expressed on HSPCs. In doing so, the likelihood of the immune system getting away from the tumor is decreased. It will also improve the safety of non-genotoxic conditioning and enable the treatment of resistant or relapsed acute myeloid leukemia.

The peer-reviewed study “Epitope editing enables targeted immunotherapy of acute myeloid leukaemia” comes from the lab of Pietro Genovese, PhD, principal investigator at the Gene Therapy Program of Dana-Farber/Boston Children’s Cancer and Blood Disorder Center and Assistant Professor of Pediatrics at Harvard Medical School, and was published today in Nature.

On-target but off-tumor toxicities

Targeting dispensable hematopoietic antigens, CAR T cells, bispecific antibodies, and antibody-drug conjugates are promising adoptive immunotherapies that can surpass traditional cancer treatments’ constraints. However, the lack of tumor-restricted markers that can be safely used limits their applicability to other hematological malignancies like acute myeloid leukemia (AML).

Since AML and normal HSPCs or differentiated myeloid cells share most of the same surface markers, on-target but off-tumor toxicities would cause myeloid aplasia and make it hard for the blood to make new blood cells. Targeting multiple surface antigens may be necessary due to the heterogeneity and flexibility of AML tumors, which raises the possibility of overlapping toxicity. To reduce the likelihood of AML eradication, a variety of AML immunotherapies are presently being developed; however, their use is likely to be limited to bridging treatment before allogeneic HSPC transplantation (HSCT).

Base editing generates stealth receptors

Postdoctoral fellow Gabriele Casirati, MD, of Genovese’s lab, and his colleagues demonstrate that tumor-associated antigens present in normal tissue can be safely targeted by altering the epitope that adoptive immunotherapies recognize in healthy cells, conferring selective resistance, and creating artificial antigens restricted to leukemia. This study focused on three epitopes: the α subunit of the IL-3 receptor (IL-3RA; also known as CD123), KIT (also known as CD117), and FMS-like tyrosine kinase 3 (FLT3; also known as CD135). These epitopes are expressed at different stages of normal hematopoietic development, and over 75% of AML cases have them. Their overexpression on AML cells is linked to a lower overall survival rate and a higher incidence of relapse after HSCT.

Casirati et al. used library screenings and epitope mapping to find amino acid changes that stop therapeutic monoclonal antibodies from binding to FLT3, CD123, and KIT. They then refined a base-editing technique to introduce these alterations into CD34+ HSPCs, which can still engraft and differentiate into various cell types for extended periods. FLT3, CD123, and KIT in HSPCs can be edited to prevent gene knockout and keep normal protein expression, regulation, and intracellular signaling. Importantly, this approach permits targeting one or more genes essential for leukemia survival, thereby producing strong anti-leukemia efficacy with low on-target/off-tumor toxicity.

Following the CAR T cell therapy, Casirati and colleagues verified that hematopoiesis edited with epitopes was resistant and that acute myeloid leukemia xenografts derived from patients were eliminated concurrently. Furthermore, they demonstrate the feasibility of multiplex epitope engineering of HSPCs, which can improve the efficacy of immunotherapies against numerous targets without causing adverse effects in other bodily regions.

Application across and beyond hematological malignancies

While improving AML treatment was the primary objective of this study, relapsed CD19 B cell acute lymphoblastic leukemia and T lymphoblastic leukemia, which have limited safe antigens, may benefit from epitope engineering treatment. Additionally, monoclonal antibodies, antibody-drug conjugates, or bi-specific T cell engagers can be used with epitope editing to gradually augment the body’s supply of genetically modified autologous cells.

Non-genotoxic conditioning for non-malignant diseases has been suggested recently using immunotherapies targeted at HSPC-specific markers. Epitope-edited HSPCs would increase HSPC engraftment in this situation, decrease the time of aplasia, and eliminate the restrictions imposed by drug pharmacokinetics. 

Furthermore, over 80% of gastrointestinal stromal tumors, colorectal cancer, small-cell lung carcinoma, and melanoma have been associated with KIT mutations. Theoretically, autologous transplantation of engineered HSPCs could make KIT-directed therapies for cancers that do not start in the blood more effective.

In conclusion, epitope editing of HSPCs can enable safer and more effective immunotherapies when on-target/off-tumor toxicities are the key limiting factors to successful clinical translation.

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