title: Clonal Dynamics In Vivo of Virus Integration Sites of T Cells Expressing a Safety Switch.
abstract: Safety switches are becoming relevant for the clinical translation of T-cell-based immunotherapies. In patients receiving an allogeneic hematopoietic stem cell transplant, the inducible caspase-9 gene (iC9) safety switch expressed by donor-derived T lymphocytes efficiently controls acute graft versus host disease (GvHD). However, in vivo elimination of iC9-T cells by the chemical inducer of dimerization (CID) that activates the iC9 protein is incomplete. To study this effect, we characterized the clonal diversity and dynamics of vector insertion sites (VIS) in iC9-T cells pre- and post-CID administration in four patients who developed GvHD. We identified 3,203 VIS among four patients and followed their in vivo clonal dynamics up to 161 days post-CID. VIS were categorized by their proximity to host genome elements, gene associations, and cis-modulatory relationship to mapped promoters. We found that VIS are preferentially located near open chromatin and promoter regions; furthermore, there was no evidence for selection bias among VIS surviving the CID treatment. The majority of iC9-T cells with high normalized VIS copy number at the time of GvHD onset were eliminated by CID, while iC9-T cells detectable post-CID generally have low normalized VIS copy number. We propose that suboptimal iC9 transgene expression is responsible for the incomplete elimination of iC9-T cells and illustrate here by simple model how cis-modulatory influences of local genome context and T-cell receptor activation status at time of CID treatment contribute to stochastic sparing of iC9-T cells.
authors.affiliation: Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA.|Houston Methodist Hospital, Houston, Texas, USA.
authors.forename: Edmund C
authors.initials: EC
authors.lastname: Chang
authors.affiliation: Biostatistics Shared Resources, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Liu
authors.affiliation: Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: West
authors.affiliation: Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA.|Houston Methodist Hospital, Houston, Texas, USA.
authors.forename: Xiaoou
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA.|Houston Methodist Hospital, Houston, Texas, USA.
authors.forename: Olga
authors.initials: O
authors.lastname: Dakhova
authors.affiliation: Human Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Wheeler
authors.affiliation: Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA.|Houston Methodist Hospital, Houston, Texas, USA.|Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA.|Department of Medicine, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Helen E
authors.initials: HE
authors.lastname: Heslop
authors.affiliation: Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA.|Houston Methodist Hospital, Houston, Texas, USA.|Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA.|Department of Medicine, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Malcolm K
authors.initials: MK
authors.lastname: Brenner
authors.affiliation: Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA.|Houston Methodist Hospital, Houston, Texas, USA.|Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.|Department of Medicine, Baylor College of Medicine, Houston, Texas, USA.|Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Gianpietro
authors.initials: G
authors.lastname: Dotti
mesh_terms: D053453:Caspase 9 / Q000235:genetics / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics; D015894:Genome, Human; D006086:Graft vs Host Disease / Q000188:drug therapy* / Q000235:genetics; D018380:Hematopoietic Stem Cell Transplantation; D006801:Humans; D007167:Immunotherapy; D009930:Organic Chemicals / Q000008:administration & dosage; D011401:Promoter Regions, Genetic; D013601:T-Lymphocytes / Q000378:metabolism* / Q000637:transplantation; D019076:Transgenes; D014184:Transplantation, Homologous; D016662:Virus Integration
chemical_list: D002843:Chromatin; D009930:Organic Chemicals; C506433:CASP9 protein, human; D053453:Caspase 9; C423866:AP 1903 reagent