Multiplex base editing to protect from CD33 directed drugs for immune and gene therapy
The selection of genetically engineered immune or hematopoietic cells in vivo after gene editing remains a clinical problem and requires a method to spare on-target toxicity to normal cells. Here, we develop a base editing approach exploiting a naturally occurring CD33 single nucleotide polymorphism leading to removal of full-length CD33 surface expression on edited cells. CD33 editing in human and nonhuman primate hematopoietic stem and progenitor cells protects myeloid progeny from CD33-targeted therapeutics without affecting normal hematopoiesis in vivo, thus demonstrating potential for improved immunotherapies with reduced off-leukemia toxicity. For broader application to gene therapies, we demonstrate highly efficient (>70%) multiplexed adenine base editing of the CD33 and gamma globin genes, resulting in long-term persistence of dual gene-edited cells with HbF reactivation in nonhuman primates. Using the CD33 antibody-drug conjugate Gemtuzumab Ozogamicin, we show resistance of engrafted, multiplex edited human cells in vivo, and a 2-fold enrichment for edited cells in vitro. Together, our results highlight the potential of adenine base editors for improved immune and gene therapies.
Authors
- Roland B. Walter (ORCID: https://orcid.org/0000-0002-9268-3341)
- Jonathan Yen (ORCID: https://orcid.org/0000-0002-9432-9450)
- Dnyanada Pande (ORCID: https://orcid.org/0000-0001-9343-0584)
- Sajeev Kohli (ORCID: https://orcid.org/0000-0001-6957-1969)
- Emily Fields (ORCID: https://orcid.org/0000-0001-7352-5260)
- Gregory A. Newby (ORCID: https://orcid.org/0000-0001-7869-2615)
- Thiyagaraj Mayuranathan (ORCID: https://orcid.org/0000-0002-9505-0363)
- Stefan Radtke (ORCID: https://orcid.org/0000-0002-2842-4820)
- Florence Borot (ORCID: https://orcid.org/0009-0001-5184-8381)
- Hans‐Peter Kiem (ORCID: https://orcid.org/0000-0001-5949-4947)
- Abdullah Mahmood Ali (ORCID: https://orcid.org/0000-0002-4007-6769)
- David R. Liu (ORCID: https://orcid.org/0000-0002-9943-7557)
- Mark Enstrom (ORCID: https://orcid.org/0000-0003-2635-3771)
- Jeffrey T. Ehmsen (ORCID: https://orcid.org/0000-0002-0403-7017)
- Siddhartha Mukherjee (ORCID: https://orcid.org/0000-0001-8251-7334)
- Mitchell J. Weiss (ORCID: https://orcid.org/0000-0002-6734-4858)
- Olivier Humbert
- George S. Laszlo (ORCID: https://orcid.org/0000-0001-8580-2659)
- Kyle Swing
Institutions
- Broad Institute (US)
- St. Jude Children's Research Hospital (US)
- Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa (ZA)
- Howard Hughes Medical Institute (US)
- Harvard University (US)
- Johns Hopkins University (US)
- Christian Medical College, Vellore (IN)
- University of Washington (US)
- Columbia University Irving Medical Center (US)
- Johns Hopkins Medicine (US)
- Fred Hutch Cancer Center (US)
- Italian Foundation of Myelodysplastic Syndromes (IT)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-05-27
- DOI
- https://doi.org/10.1038/s41467-025-59713-2
- Citations
- 8
- Primary Topic
- CRISPR and Genetic Engineering
- Type
- article
- Field-Weighted Citation Impact
- 6.45
Funders
- Howard Hughes Medical Institute
- American Lebanese Syrian Associated Charities
- Department of Biotechnology, Ministry of Science and Technology, India
- National Institutes of Health
- National Cancer Institute