Precision T cell correction platform for inborn errors of immunity

Molecular Therapy, vol. 33, pp. 5624–5643

Abstract

CRISPR-Cas9 gene editing is a promising tool to correct pathogenic variants for autologous cell therapies targeting inborn errors of immunity (IEI). Current strategies, such as gene knockout or cDNA knockin, address many single-gene defects but can disrupt gene expression, highlighting the need for precise correction platforms. While transplanting corrected autologous hematopoietic stem cells is a curative approach, it is unsuitable for patients with advanced disease, inflammation, or acute infections. As correcting T cells is an alternative therapeutic strategy for lymphoid IEIs, we present an efficient T cell single-nucleotide variant (SNV) correction platform based on homology-directed repair (HDR). By using STAT1 gain-of-function, cartilage hair hypoplasia, deficiency of ADA2, and autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy as IEI models, we demonstrate that our platform achieves up to 80% correction, with resultant functional correction of the disease phenotype in the selected models. Furthermore, we performed safety profiling using GUIDE-seq, single-cell RNA sequencing, long-read genome sequencing, and proteomics analysis and detected no genomic, transcriptomic, or proteomic aberrations. This study establishes HDR-based SNV editing as a portable method for developing clinical autologous T cell therapies and represents a promising step toward a broad-spectrum gene correction platform for treating diverse monogenic immune disorders.

Authors 29

1. Katariina Mamia

   Oslo University Hospital · University of Oslo

   Affiliation as printed

   Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway; Department of Pediatrics, Oslo University Hospital, 0372 Oslo, Norway; Precision Immunotherapy Alliance, University of Oslo, 0379 Oslo, Norway

   Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway; Department of Pediatrics, Oslo University Hospital; Oslo, 0372, Norway; Precision Immunotherapy Alliance, University of Oslo; Oslo, 0379, Norway

2. Solrun Kolbeinsdottir

   Karolinska Institutet

   Affiliation as printed

   Department of Oncology-Pathology, Karolinska Institutet, 17177 Stockholm, Sweden

   Department of Oncology-Pathology, Karolinska Institutet; Stockholm, 17177, Sweden

3. Kornel Labun

   University of Bergen

   Affiliation as printed

   Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway

   Computational Biology Unit, Department of Informatics, University of Bergen; Bergen, 5008, Norway

4. Zhuokun Li

   University of Oslo

   Affiliation as printed

   Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway

   Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway

5. Anna Zofia Komisarczuk

   University of Oslo

   Affiliation as printed

   Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway; Precision Immunotherapy Alliance, University of Oslo, 0379 Oslo, Norway

   Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway; Precision Immunotherapy Alliance, University of Oslo; Oslo, 0379, Norway

6. Salla Keskitalo

   University of Helsinki · HiLIFE – Elämäntieteiden Instituutti

   Affiliation as printed

   Systems Biology/Pathology Research Group, University of Helsinki, 00014 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland

   Systems Biology/Pathology Research Group, University of Helsinki; Helsinki, 00014, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki; Helsinki, 00014, Finland

7. Ganna Reint

   University of Oslo

   Affiliation as printed

   Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway

   Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway

8. Britt Olaug Lindestad

   University of Oslo

   Affiliation as printed

   Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway; Precision Immunotherapy Alliance, University of Oslo, 0379 Oslo, Norway

   Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway; Precision Immunotherapy Alliance, University of Oslo; Oslo, 0379, Norway

9. Thea Johanne Gjerdingen

   Oslo University Hospital · University of Oslo

   Affiliation as printed

   Precision Immunotherapy Alliance, University of Oslo, 0379 Oslo, Norway; Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway

   Precision Immunotherapy Alliance, University of Oslo; Oslo, 0379, Norway; Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet; Oslo, 0310, Norway

10. Antti Tuhkala

    University of Helsinki · HiLIFE – Elämäntieteiden Instituutti

    Affiliation as printed

    Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland

    Institute of Biotechnology, HiLIFE, University of Helsinki; Helsinki, 00014, Finland

11. Carolina Wieczorek Ervik

    University of Oslo

    Affiliation as printed

    Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway; Precision Immunotherapy Alliance, University of Oslo, 0379 Oslo, Norway

    Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway; Precision Immunotherapy Alliance, University of Oslo; Oslo, 0379, Norway

12. Pavel Kopcil

    University of Oslo

    Affiliation as printed

    Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway; Precision Immunotherapy Alliance, University of Oslo, 0379 Oslo, Norway

    Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway; Precision Immunotherapy Alliance, University of Oslo; Oslo, 0379, Norway

13. Nail Fatkhutdinov

    University of Oslo

    Affiliation as printed

    Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway

    Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway

14. Karen Helene Bronken Martinsen

    Oslo University Hospital · University of Oslo

    Affiliation as printed

    Division of Pediatric and Adolescent Medicine, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, 0424 Oslo, Norway; Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway

    Division of Pediatric and Adolescent Medicine, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, 0424, Norway; Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, 0318, Norway

15. Hans Christian Erichsen

    Oslo University Hospital · University of Oslo

    Affiliation as printed

    Division of Pediatric and Adolescent Medicine, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, 0424 Oslo, Norway; Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway

    Division of Pediatric and Adolescent Medicine, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, 0424, Norway; Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, 0318, Norway

16. Monika Szymańska

    University of Oslo

    Affiliation as printed

    Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway; Precision Immunotherapy Alliance, University of Oslo, 0379 Oslo, Norway

    Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway; Precision Immunotherapy Alliance, University of Oslo; Oslo, 0379, Norway

17. Virpi Glumoff

    Oulu University Hospital · University of Oulu

    Affiliation as printed

    Research Unit of Internal Medicine and Biomedicine, University of Oulu, 90014 Oulu, Finland; ERN-RITA Core Center Member, RITAFIN Consortium, Infectious Diseases Clinic, Oulu University Hospital, 90220 Oulu, Finland

    Research Unit of Internal Medicine and Biomedicine, University of Oulu; Oulu, 90014, Finland; ERN-RITA Core Center Member, RITAFIN Consortium, Infectious Diseases Clinic, Oulu University Hospital; Oulu, 90220, Finland

18. Janna Saarela

    Oslo University Hospital · University of Oslo · Institute for Molecular Medicine Finland · HiLIFE – Elämäntieteiden Instituutti

    Affiliation as printed

    Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway; Institute for Molecular Medicine Finland, HiLIFE, 00290 Helsinki, Finland; Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway

    Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway; Institute for Molecular Medicine Finland, HiLIFE; Helsinki, 00290, Finland; Department of Medical Genetics, Oslo University Hospital; Oslo, 0450, Norway

19. Trond Melbye Michelsen

    Oslo University Hospital

    Affiliation as printed

    Department of Obstetrics, Division of Obstetrics and Gynecology, Oslo University Hospital, 0424 Oslo, Norway

    Department of Obstetrics, Division of Obstetrics and Gynecology, Oslo University Hospital; Oslo, 0424, Norway

20. Camilla Schalin‐Jäntti Aachen

    University of Helsinki · Helsinki University Hospital · Endo-ERN

    Affiliation as printed

    Endocrinology, Abdominal Center, Helsinki University Hospital, 00029 Helsinki, Finland; University of Helsinki, ENDO-ERN (European Reference Network on Rare Endocrine Conditions), 00290 Helsinki, Finland

    Endocrinology, Abdominal Center, Helsinki University Hospital; Helsinki, 00029, Finland; University of Helsinki, ENDO-ERN (European Reference Network on Rare Endocrine Conditions); Helsinki, 00290, Finland

21. Johanna Olweus

    Oslo University Hospital · University of Oslo

    Affiliation as printed

    Precision Immunotherapy Alliance, University of Oslo, 0379 Oslo, Norway; Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway

    Precision Immunotherapy Alliance, University of Oslo; Oslo, 0379, Norway; Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet; Oslo, 0310, Norway

22. Eira Leinonen

    University of Helsinki

    Affiliation as printed

    Folkhälsan Institute of Genetics, and Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland

    Folkhälsan Institute of Genetics, and Stem Cells and Metabolism Research Program, University of Helsinki; Helsinki, 00014, Finland

23. Markku T Varjosalo

    University of Helsinki · HiLIFE – Elämäntieteiden Instituutti

    Affiliation as printed

    Systems Biology/Pathology Research Group, University of Helsinki, 00014 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland

    Systems Biology/Pathology Research Group, University of Helsinki; Helsinki, 00014, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki; Helsinki, 00014, Finland

24. Eivind Valen

    University of Oslo · University of Bergen

    Affiliation as printed

    Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway; Department of Biosciences, University of Oslo, 0371 Oslo, Norway

    Computational Biology Unit, Department of Informatics, University of Bergen; Bergen, 5008, Norway; Department of Biosciences, University of Oslo; Oslo, 0371, Norway

25. Timo Hautala

    Oulu University Hospital · University of Oulu

    Affiliation as printed

    Research Unit of Internal Medicine and Biomedicine, University of Oulu, 90014 Oulu, Finland; ERN-RITA Core Center Member, RITAFIN Consortium, Infectious Diseases Clinic, Oulu University Hospital, 90220 Oulu, Finland

    Research Unit of Internal Medicine and Biomedicine, University of Oulu; Oulu, 90014, Finland; ERN-RITA Core Center Member, RITAFIN Consortium, Infectious Diseases Clinic, Oulu University Hospital; Oulu, 90220, Finland

26. Martin Enge

    Karolinska Institutet

    Affiliation as printed

    Department of Oncology-Pathology, Karolinska Institutet, 17177 Stockholm, Sweden

    Department of Oncology-Pathology, Karolinska Institutet; Stockholm, 17177, Sweden

27. Timi J. Martelius

    University of Helsinki · Helsinki University Hospital

    Affiliation as printed

    Inflammation Center, Department of Infectious Disease, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland

    Inflammation Center, Department of Infectious Disease, Helsinki University Hospital and University of Helsinki; Helsinki, 00029, Finland

28. Shiva Dahal‐Koirala

    University of Oslo

    Affiliation as printed

    Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway; Precision Immunotherapy Alliance, University of Oslo, 0379 Oslo, Norway

    Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway; Precision Immunotherapy Alliance, University of Oslo; Oslo, 0379, Norway. Electronic address: e.m.haapaniemi@ncmm.uio.no

29. Emma Maria Haapaniemi corresponding

    Oslo University Hospital · University of Oslo

    Affiliation as printed

    Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway; Department of Pediatrics, Oslo University Hospital, 0372 Oslo, Norway; Precision Immunotherapy Alliance, University of Oslo, 0379 Oslo, Norway. Electronic address: e.m.haapaniemi@ncmm.uio.no

    Centre for Molecular Medicine Norway, University of Oslo; Oslo, 0318, Norway; Precision Immunotherapy Alliance, University of Oslo; Oslo, 0379, Norway. Electronic address: e.m.haapaniemi@ncmm.uio.no