Persistent hematopoietic polyclonality after lentivirus-mediated gene therapy for Fabry disease

Amr H Saleh; Michael Rothe; Dwayne L Barber; William M McKillop; Graeme Fraser; Chantal F Morel; Axel Schambach; Christiane Auray-Blais; Michael L West; Aneal Khan; Daniel H Fowler; C Anthony Rupar; Ronan Foley; Jeffrey A Medin; Armand Keating

doi:10.1016/j.omtm.2023.01.003

Persistent hematopoietic polyclonality after lentivirus-mediated gene therapy for Fabry disease

Mol Ther Methods Clin Dev. 2023 Jan 18:28:262-271. doi: 10.1016/j.omtm.2023.01.003. eCollection 2023 Mar 9.

Authors

Amr H Saleh^{1

2}, Michael Rothe³, Dwayne L Barber^{1

4}, William M McKillop⁵, Graeme Fraser⁶, Chantal F Morel⁷, Axel Schambach^{3

8}, Christiane Auray-Blais⁹, Michael L West¹⁰, Aneal Khan¹¹, Daniel H Fowler¹², C Anthony Rupar^{13

14}, Ronan Foley¹⁵, Jeffrey A Medin^{5

16}, Armand Keating^{1

4

17}

Affiliations

¹ University Health Network, Toronto, ON, Canada.
² Department of Medicine, University of Alberta, Edmonton, AB, Canada.
³ Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.
⁴ Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
⁵ Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.
⁶ Department of Oncology, McMaster University and Juravinski Hospital and Cancer Centre, Hamilton, ON, Canada.
⁷ Fred A. Litwin Family Centre in Genetic Medicine, Department of Medicine, University, Health Network, Toronto, ON, Canada.
⁸ Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
⁹ Division of Medical Genetics, Department of Pediatrics, CIUSSS de l'Estrie-CHUS, Hospital Fleurimont, Université de Sherbrooke, Sherbrooke, QC, Canada.
¹⁰ Division of Nephrology, Department of Medicine, Dalhousie University, Halifax, NS, Canada.
¹¹ Department of Medical Genetics, Metabolics and Pediatrics, Alberta Children's Hospital, Cumming School of Medicine, Research Institute, University of Calgary, Calgary, AB, Canada.
¹² Rapa Therapeutics, Rockville, MD, USA.
¹³ Departments of Pathology and Laboratory Medicine and Pediatrics, Western University, London, ON, Canada.
¹⁴ Children's Health Research Institute, London, ON, Canada.
¹⁵ Department of Pathology and Molecular Medicine, McMaster University and Juravinski, Hospital and Cancer Centre, Hamilton, ON, Canada.
¹⁶ Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
¹⁷ Princess Margaret Cancer Centre, 610 University Avenue, 700U 6-325 Toronto, ON M5G 2M9, Canada.

Abstract

The safety and efficacy of lentivirus-mediated gene therapy was recently demonstrated in five male patients with Fabry disease-a rare X-linked lysosomal storage disorder caused by GLA gene mutations that result in multiple end-organ complications. To evaluate the risks of clonal dominance and leukemogenesis, which have been reported in multiple gene therapy trials, we conducted a comprehensive DNA insertion site analysis of peripheral blood samples from the five patients in our gene therapy trial. We found that patients had a polyclonal integration site spectrum and did not find evidence of a dominant clone in any patient. Although we identified vector integrations near proto-oncogenes, these had low percentages of contributions to the overall pool of integrations and did not persist over time. Overall, we show that our trial of lentivirus-mediated gene therapy for Fabry disease did not lead to hematopoietic clonal dominance and likely did not elevate the risk of leukemogenic transformation.

Keywords: Fabry disease; clinical trial; gene therapy; lentiviral integration; lentiviral safety.