Human T cell generation is restored in CD3δ severe combined immunodeficiency through adenine base editing

Grace E McAuley; Gloria Yiu; Patrick C Chang; Gregory A Newby; Beatriz Campo-Fernandez; Sorel T Fitz-Gibbon; Xiaomeng Wu; Sung-Hae L Kang; Amber Garibay; Jeffrey Butler; Valentina Christian; Ryan L Wong; Kelcee A Everette; Anthony Azzun; Hila Gelfer; Christopher S Seet; Aru Narendran; Luis Murguia-Favela; Zulema Romero; Nicola Wright; David R Liu; Gay M Crooks; Donald B Kohn

doi:10.1016/j.cell.2023.02.027

Human T cell generation is restored in CD3δ severe combined immunodeficiency through adenine base editing

Cell. 2023 Mar 30;186(7):1398-1416.e23. doi: 10.1016/j.cell.2023.02.027. Epub 2023 Mar 20.

Authors

Grace E McAuley¹, Gloria Yiu², Patrick C Chang³, Gregory A Newby⁴, Beatriz Campo-Fernandez¹, Sorel T Fitz-Gibbon⁵, Xiaomeng Wu¹, Sung-Hae L Kang³, Amber Garibay³, Jeffrey Butler³, Valentina Christian³, Ryan L Wong⁶, Kelcee A Everette⁴, Anthony Azzun¹, Hila Gelfer¹, Christopher S Seet⁷, Aru Narendran⁸, Luis Murguia-Favela⁸, Zulema Romero¹, Nicola Wright⁸, David R Liu⁴, Gay M Crooks⁹, Donald B Kohn¹⁰

Affiliations

¹ Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
² Department of Medicine, Division of Rheumatology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
³ Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁴ Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
⁵ Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁶ Department of Molecular & Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁷ Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁸ Department of Pediatrics, University of Calgary, Calgary, AB T2N 1N4, Canada.
⁹ Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of Pediatric Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
¹⁰ Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular & Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of Pediatric Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: dkohn1@mednet.ucla.edu.

Abstract

CD3δ SCID is a devastating inborn error of immunity caused by mutations in CD3D, encoding the invariant CD3δ chain of the CD3/TCR complex necessary for normal thymopoiesis. We demonstrate an adenine base editing (ABE) strategy to restore CD3δ in autologous hematopoietic stem and progenitor cells (HSPCs). Delivery of mRNA encoding a laboratory-evolved ABE and guide RNA into a CD3δ SCID patient's HSPCs resulted in a 71.2% ± 7.85% (n = 3) correction of the pathogenic mutation. Edited HSPCs differentiated in artificial thymic organoids produced mature T cells exhibiting diverse TCR repertoires and TCR-dependent functions. Edited human HSPCs transplanted into immunodeficient mice showed 88% reversion of the CD3D defect in human CD34+ cells isolated from mouse bone marrow after 16 weeks, indicating correction of long-term repopulating HSCs. These findings demonstrate the preclinical efficacy of ABE in HSPCs for the treatment of CD3δ SCID, providing a foundation for the development of a one-time treatment for CD3δ SCID patients.

Keywords: CD3D severe combined immune deficiency; CITE-seq; artificial thymic organoid; base editing; hematopoietic stem and progenitor cells.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
CD3 Complex
Gene Editing
Humans
Mice
Mice, SCID
Receptors, Antigen, T-Cell / genetics
Severe Combined Immunodeficiency* / genetics
Severe Combined Immunodeficiency* / therapy
T-Lymphocytes*

Substances

CD3 Complex
Receptors, Antigen, T-Cell

Abstract

Publication types

MeSH terms

Substances

Grants and funding