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

Genome Med 2018 09 28;10(1):70. Epub 2018 Sep 28.

Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.

Background: 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. 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.

Methods: Here 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.

Results: Comparison 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.

Conclusions: This 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.

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13073-018-0580-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161392PMC
September 2018
55 Reads

Publication Analysis

Top Keywords

gene therapy
20
metagenomic analysis
12
cell
11
gene
9
analysis microbial
8
therapy scid-x1
8
antibiotic resistance
8
severe combined
8
microbial populations
8
estimation numbers
8
scid-x1 gene
8
cell divisions
8
analysis
6
populations
5
therapy
5
oropharyngeal nasopharyngeal
4
nasopharyngeal gut
4
populations oropharyngeal
4
repertoire reconstitution
4
comparison progenitor
4

References

(Supplied by CrossRef)

A Aiuti et al.
Science 2002

A Aiuti et al.
J Clin Invest 2007

A Aiuti et al.
Science 2013

A Biffi et al.
Science 2013

M Cavazzana-Calvo et al.
Br J Haematol 2013

S Hacein-Bey-Abina et al.
N Engl J Med 2002

HB Gaspar et al.
Lancet 2004

S Hacein-Bey-Abina et al.
N Engl J Med 2010

HB Gaspar et al.
Sci Transl Med 2011

M Noguchi et al.
Cell 1993

JM Puck et al.
Hum Mol Genet 1993

Similar Publications