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

Erik L Clarke,David A Williams,Alain Fischer,Rebecca Marsh,Casey E Hofstaedter,Myriam Armant,Donald B Kohn,Judith R Kelsen ,Young Sun Hwang ,Andrew Jesse Connell ,J.k Everett ,Salima Hacein‐Bey‐Abina ,Arwa Abbas ,Sung-Yun Pai,Luigi D Notarangelo,Marina Cavazzana,Ronald G Collman,Emmanuelle Six,Nadia A Kadry,Frederic D Bushman

doi:10.1186/s13073-018-0580-z

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.

Highlights

Mutation of the Interleukin 2 receptor subunit gamma (IL2RG) gene results in a form of severe combined immune deficiency (SCID-X1), which has been treated successfully with hematopoietic stem cell gene therapy
Metagenomic analysis revealed enrichment of genes for antibiotic resistance in gene-corrected subjects relative to healthy controls, likely a result of higher healthcare exposure. This multi-omic approach enables the characterization of multiple effects of X-linked severe combined immunodeficiency (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
Experimental strategy Our comparative analysis of gene-corrected progenitors and daughter T cells focused on nine patients from the Second SCID gene therapy trial (SCIDn2) trial [19] and five patients from the First SCID gene therapy trial (SCIDn1) trial [8] for whom samples were available (Fig. 1a)

Summary

Introduction

Mutation 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. Several primary immunodeficiencies have been treated successfully by gene correction of hematopoietic stem cells (HSC) with integrating vectors [1,2,3,4,5,6,7,8,9] This therapeutic strategy has benefited many patients and in addition provides a unique window to study mechanisms associated with immune reconstitution. In the first gene therapy trial to treat SCID-X1 (denoted here “SCIDn1”), early designs of gammaretroviral vectors were used [6,7,8,9], which were the only vector type available at the time These vectors contained strong enhancers as part of the long terminal repeat (LTR) of the Moloney murine leukemia virus (MLV) retroviral backbone. Subsequent experience implicated these vectors in insertional mutagenesis, in which vector signals activated transcription of host proto-oncogenes, in some cases associated with severe adverse events [16,17,18]

Methods

Results

Discussion

Conclusion