T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency

Abstract

BackgroundMutation of the IL2RG gene results in a form of severe combined immune deficiency (SCID-X1), which has been treated successfully with hematopoietic stem cell gene therapy. SCID-X1 gene therapy results in reconstitution of the previously lacking T cell compartment, allowing analysis of the roles of T cell immunity in humans by comparing before and after gene correction.MethodsHere we interrogate T cell reconstitution using four forms of high throughput analysis. (1) Estimation of the numbers of transduced progenitor cells by monitoring unique positions of integration of the therapeutic gene transfer vector. (2) Estimation of T cell population structure by sequencing of the recombined T cell receptor (TCR) beta locus. (3) Metagenomic analysis of microbial populations in oropharyngeal, nasopharyngeal, and gut samples. (4) Metagenomic analysis of viral populations in gut samples.ResultsComparison of progenitor and mature T cell populations allowed estimation of a minimum number of cell divisions needed to generate the observed populations. Analysis of microbial populations showed the effects of immune reconstitution, including normalization of gut microbiota and clearance of viral infections. Metagenomic analysis revealed enrichment of genes for antibiotic resistance in gene-corrected subjects relative to healthy controls, likely a result of higher healthcare exposure.ConclusionsThis multi-omic approach enables the characterization of multiple effects of SCID-X1 gene therapy, including T cell repertoire reconstitution, estimation of numbers of cell divisions between progenitors and daughter T cells, normalization of the microbiome, clearance of microbial pathogens, and modulations in antibiotic resistance gene levels. Together, these results quantify several aspects of the long-term efficacy of gene therapy for SCID-X1. This study includes data from ClinicalTrials.gov numbers NCT01410019, NCT01175239, and NCT01129544.Electronic supplementary materialThe online version of this article (10.1186/s13073-018-0580-z) contains supplementary material, which is available to authorized users.

Gene therapy for severe combined immunodeficiencies and beyond

“…These data made it possible to estimate the average number of cell divisions each transduced clone had undergone before rearrangement of the TCRB locus during thymus differentiation. The value is ∼10; this fits with the estimate for the SCID X1 revertant discussed above (Bousso et al, 2000; Clarke et al, 2018; Fig. 2).…”

“…The next question relates to T cell diversity. High-throughput sequencing of T cell receptor beta chain (TCRB) variable diversity joining segments from blood T cells of patients treated in trials 1 or 2 showed that distribution of TCR VB (variable region of TCRB) and JB (joining region of TCRB) element usage and the number of unique TCRB CDR3 sequences were similar to control values in all but one of the seven patients tested (Clarke et al, 2018). These data made it possible to estimate the average number of cell divisions each transduced clone had undergone before rearrangement of the TCRB locus during thymus differentiation.…”

“…An IS analysis of the treated patients’ T cells indicated that there were ∼1,000 unique ISs, as estimated using Chao’s methodology (Hacein-Bey-Abina et al, 2010; Clarke et al, 2018). After ≤20 yr of follow-up, the number of ISs was found to be quite stable.…”

“…After ≤20 yr of follow-up, the number of ISs was found to be quite stable. Furthermore, the number was in line with the Shannon diversity index, which also takes account of the abundance of clones (Clarke et al, 2018). Thus, the blood T cell population has derived from no more than 1,000 transduced progenitor cells.…”

The γc Family of Cytokines: Basic Biology to Therapeutic Ramifications

“…While successful in substantially improving immune function, two individuals developed acute lymphocytic leukemia resulting from retroviral insertion and activation of the LMO2 proto-oncogene (Hacein-Bey-Abina et al, 2003). Fortunately, the leukemias in turn were successfully treated, but these serious adverse events resulted in work to develop alternative strategies to achieve the beneficial results while preventing or reducing untoward effects (Hacein-Bey-Abina et al, 2014;Clarke et al, 2018). Gene therapeutic approaches for JAK3-deficient and IL7R-deficient SCID are areas for future development.…”