Long-term robustness of a T-cell system emerging from somatic rescue of a genetic block in T-cell development

Abstract

Backgound The potential of a single progenitor cell to establish and maintain long-term protective T-cell immunity in humans is unknown. For genetic disorders disabling T-cell immunity, somatic reversion was shown to support limited T-cell development attenuating the clinical phenotype. However, the cases reported so far deteriorated over time leaving unanswered the important question of long-term activity of revertant precursors and the robustness of the resulting T-cell system. Methods We applied TCRβ-CDR3 sequencing and mass cytometry on serial samples of a now 18 year-old SCIDX1 patient with somatic reversion to analyse the longitudinal diversification and stability of a T-cell system emerging from somatic gene rescue. Findings We detected close to 10 5 individual CDR3β sequences in the patient. Blood samples of equal size contained about 10-fold fewer unique CDR3β sequences compared to healthy donors, indicating a surprisingly broad repertoire. Despite dramatic expansions and contractions of individual clonotypes representing up to 30% of the repertoire, stable diversity indices revealed that these transient clonal distortions did not cause long-term repertoire imbalance. Phenotypically, the T-cell system did not show evidence for progressive exhaustion. Combined with immunoglobulin substitution, the limited T-cell system in this patient supported an unremarkable clinical course over 18 years. Interpretation Genetic correction in the appropriate cell type, in our patient most likely in a T-cell biased self-renewing hematopoietic progenitor, can yield a diverse T-cell system that provides long-term repertoire stability, does not show evidence for progressive exhaustion and is capable of providing protective and regulated T-cell immunity for at least two decades. Funding DFG EH 145/9-1, DFG SCHW 432/4-1 and the German Research Foundation under Germany's Excellence Strategy–EXC-2189–Project ID: 390939984.

Somatic Reversion of a Novel IL2RG Mutation Resulting in Atypical X-Linked Combined Immunodeficiency

“…Even though the reversion is observed in all three siblings, differences in their genetics, epigenetic profile and environmental conditions might explain the disparity between P1 symptoms and the rest of the brothers. We conclude that the reversion allows the restoration of T-cell function and immunity for at least 26 years of P1 who is the longest surviving case in comparison with atypical X-SCID patients reported with IL2RG reversion till now [ 10 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 ]. The precursor cells from the patients were not studied nor analyzed in this study due to ethical reasons.…”

“…It can be widely observed that reverted mutations in the IL2RG gene can display within a large range of clinical and immunological findings. Patients with low T- and NK-cell counts are documented with T452C, A284-15G and T455C mutations [ 10 , 17 , 23 ], normal STAT5 phosphorylation is reported for a patient with T466C mutation [ 19 ], and even normal TCR repertoire in patients with A655T and T343C mutations [ 16 , 20 ]. Therefore, it is important to underline the differential diagnosis of SCID variants in terms of functional and clinical characterization beyond the infant period.…”

“…Lately, an increasing number of studies have identified revertant somatic mosaicism in patients affected with PIDs, in which the co-existence of mutant and revertant cells has been described [ 14 ]. To the best of our knowledge, only a few cases of X-SCID have been reported with revertant mutations in the IL2RG gene revealing somatic mosaicism [ 10 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 ]. All of these patients have a significant attenuation of the clinical phenotype since there are variable reverted mutations within lymphocyte sub-populations.…”

Challenges in Gene Therapy for Somatic Reverted Mosaicism in X-Linked Combined Immunodeficiency by CRISPR/Cas9 and Prime Editing

“…The fact that the reversion was not observable in the Sanger sequencing of the PBMCs or, more specifically, in other lymphocyte types (such as NK cells or B cells) and phagocytic cells (like monocytes or macrophages) led us to assume that the natural reversion only occurred in early progenitor T cells and was absent in hematopoietic stem cells. Although the clinical benefit of immune reconstitution in X-SCID patients with reverted mosaicism is improved by the presence of revertant cells [ 5 , 6 , 7 , 8 , 9 , 11 ], the illness progression of several patients still worsened with age [ 10 , 12 ]. As a result, the stability of revertant cells is not assured.…”

“…Without any treatment, the risk of death is very high within the first year of life [ 2 , 3 ]. On the other hand, atypical X-SCID patients present a milder form of immunodeficiency due to either hypomorphic mutations [ 4 ] or natural correction induced by somatic reversions [ 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. The current treatment of X-SCID includes prophylaxis for infections to ensure the safety of patients and hematopoietic stem cell transplantation (HSCT) to reconstruct their immune function [ 2 ].…”