In vivo tracking of T cells in humans unveils decade-long survival and activity of genetically modified T memory stem cells

Abstract

A definitive understanding of survival and differentiation potential in humans of T cell subpopulations is of paramount importance for the development of effective T cell therapies. In particular, uncovering the dynamics in vivo in humans of the recently described T memory stem cells (TSCM) would be crucial for therapeutic approaches that aim at taking advantage of a stable cellular vehicle with precursor potential. We exploited data derived from two gene therapy clinical trials for an inherited immunodeficiency, using either retrovirally engineered hematopoietic stem cells or mature lymphocytes to trace individual T cell clones directly in vivo in humans. We compared healthy donors and bone marrow-transplanted patients, studied long-term in vivo T cell composition under different clinical conditions, and specifically examined TSCM contribution according to age, conditioning regimen, disease background, cell source, long-term reconstitution, and ex vivo gene correction processing. High-throughput sequencing of retroviral vector integration sites (ISs) allowed tracing the fate of more than 1700 individual T cell clones in gene therapy patients after infusion of gene-corrected hematopoietic stem cells or mature lymphocytes. We shed light on long-term in vivo clonal relationships among different T cell subtypes, and we unveiled that TSCM are able to persist and to preserve their precursor potential in humans for up to 12 years after infusion of gene-corrected lymphocytes. Overall, this work provides high-resolution tracking of T cell fate and activity and validates, in humans, the safe and functional decade-long survival of engineered TSCM, paving the way for their future application in clinical settings.

Prolonged Antiretroviral Therapy Preserves HIV-1-Specific CD8 T Cells with Stem Cell-Like Properties

“…This view is supported by data from two long-term gene therapy clinical trials demonstrating that these T memory stem cells are able to persist and preserve their precursor potential for up to 12 years, consistent with the critical role of these cells for maintaining lifelong pathogen-specific immune defense (24). Moreover, CD4 T SCM cells have recently been shown to provide an important cellular source of HIV-1 long-term persistence, further supporting the role of T SCM cells as extremely long-lasting memory cells (31,32).…”

“…Simultaneously, T memory stem cells can give rise to more differentiated central memory T cells (T CM cells), effector memory T cells (T EM cells), and terminally differentiated effector memory T cells (T TDEM cells) through transitional proliferation and effectively reconstitute cellular immunity in immunocompromised hosts during serial transplantation experiments in animal models (23). A recent study also showed that T SCM cells are able to persist and to preserve their precursor potential for up to 12 years after lymphocyte infusion in immunodeficient patients (24) and play important roles for regenerating the memory T cell pool after hematopoietic stem cell transplantation (25,26). So far, T memory stem cells recognizing influenza virus (Flu), cytomegalovirus (CMV), and tumor antigens have been identified (20), but it is likely that T memory stem cells contribute to cellular immune responses against virtually any type of antigen.…”

“…Since CD8 T SCM cells have enhanced abilities to persist long term and do not seem to depend on continuous antigenic challenge for their survival (22,24), they may become enriched during prolonged periods of antiretroviral therapy. To analyze this, we individually assessed the proportions of HIV-1-specific CD8 T SCM cells in ART-treated patients stratified according to their duration of antiretroviral therapy.…”

Neonatal thymectomy reveals differentiation and plasticity within human naive T cells

“…These Tscm are suggested to be long lived and endowed with differentiation potential and self-renewal abilities, as they can generate effector/memory T cell subsets while preserving the original naive-like phenotype (25). Recent human in vivo analysis has suggested that relative Tscm frequencies do not vary much with age, but could increase to compensate for reduced naive T cell output (31). The increased Tscm compartment after neonatal thymectomy could therefore be compensatory for the reduced naive T cell compartment and aid in the expansion of the Tcm and Tem compartments to normal levels.…”

Gene-corrected human Munc13-4–deficient CD8+ T cells can efficiently restrict EBV-driven lymphoproliferation in immunodeficient mice

“…In a clinical trial of T-cell gene therapy for adenosine deaminase deficiency, the transduced T cells persisted in the circulation for up to 12 years after infusion 13 as a result of efficient transduction, in vitro expansion, and the in vivo persistence of T SCM . In the present study, we confirmed the presence of T SCM within the T-cell pool from FHL3 patients (supplemental Figure 2A).…”