Long-term assessment of haematological recovery following somatic genetic rescue in a MYSM1-deficient patient: Implications for in vivo gene therapy

Abstract

MYSM1 deficiency causes inherited bone marrow failure syndrome (IBMFS). We have previously identified an IBMFS patient with a homozygous pathogenic variant in MYSM1 who recovered from cytopenia due to spontaneous correction of one MYSM1 variant in the haematopoietic compartment, an event called somatic genetic rescue (SGR). The study of the genetic and biological aspects of the patient's haematopoietic/lymphopoietic system over a decade after SGR shows that one genetically corrected haematopoietic stem cell (HSC) can restore a healthy and stable haematopoietic system. This supports in vivo gene correction of HSCs as a promising treatment for IBMFS, including MYSM1 deficiency.

Keywords: MYSM1; bone marrow failure; haematopoiesis; natural gene therapy; somatic genetic rescue.

FIGURE 1

Activity of the H656R MYSM1 variant and haematological parameters in the patient over time. (A) Schematic representation of the full‐length MYSM1 protein as well as the WT and the mutated forms of the C‐terminal part of MYSM1 (noted C1‐WT and C1‐H656R, respectively) used to assess the deubiquitinase activity in vitro. (B) A 6% polyacrylamide gel stained with Coomassie blue showing fractions from a representative purification of GST‐C1‐WT and GST‐C1‐H656R used in in vitro deubiquitinase assay. Glut: Glutathione purification. (C) Fluorescence intensity measurements for C1‐WT (green line), C1‐H656R (red line), UCHL‐1 used as positive control (blue line) and Ub‐AMC alone used as background fluorescence control (black line). (D) Whole blood cell counts over time. Grey areas represent normal values obtained in age‐matched healthy subjects. (E) Immunophenotyping of the B cell compartment in the patient 12 years post‐somatic genetic rescue (SGR) and serology values post‐vaccination and post‐infection. Age‐matched normal values are indicated in brackets.

FIGURE 2

Immunological phenotype of patient's blood 12 years post‐somatic genetic rescue (SGR) and SGR detection by next‐generation sequencing (NGS). (A) Representative illustration of uniform manifold approximation and projection applied to analyse immune cell subsets from whole blood samples obtained in one age‐matched healthy control and the MYSM1‐deficient patient 12 years post‐SGR. Each cluster is visually represented by a distinct colour. The arrow highlights the T γδ cell population in patient. (B) Proportion of the immunological subsets obtained in blood from five age‐matched healthy controls and the patient 12 years post‐SGR. (C) Proportion of naive and memory B and T cell populations in the patient 12 years post‐SGR and 5 age‐matched healthy controls. (D) Graphic representation of the numbers of WT and MYSM1 c.1967A>G mutated reads obtained by NGS in the indicated cell populations. (E) Graphic representation of the estimated proportion of SGR⁺ cell subpopulations deduced from (D). PBMNCs, peripheral blood mononuclear cells. Statistical significance: *p < 0.05; **p < 0.01; ns, not significant.