An in vivo genetic reversion highlights the crucial role of Myb-Like, SWIRM, and MPN domains 1 (MYSM1) in human hematopoiesis and lymphocyte differentiation

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An in vivo genetic reversion highlights the crucial role of Myb-Like, SWIRM, and MPN domains 1 (MYSM1) in human hematopoiesis and lymphocyte differentiation Tangui Le Guen, PhD, Fabien Touzot, MD, PhD, Isabelle André-Schmutz, PhD, Chantal Lagresle-Peyrou, PhD, Benoit France, MSc, Laetitia Kermasson, Nathalie Lambert, Capucine Picard, MD, PhD, Patrick Nitschke, PhD, Wassila Carpentier, PhD, Christine Bole- Feysot, PhD, Annick Lim, PhD, Marina Cavazzana, MD, PhD, Isabelle Callebaut, PhD, Jean Soulier, MD, PhD, Nada Jabado, MD, PhD, Alain Fischer, MD, PhD, Jean-Pierre de Villartay, PhD, Patrick Revy, PhD Journal of Allergy and Clinical Immunology Volume 136, Issue 6, Pages 1619-1626.e5 (December 2015) DOI: 10.1016/j.jaci.2015.06.008 Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 1 Phenotypic analysis of bone marrow cells. A and B, Bone marrow smear reveals hypocellular bone marrow with a paucity of erythroid precursors (erythroblasts) in the patient at 5 months of age (Fig 1, B) compared with a 15 month-old-control subject (Fig 1, A) by using May-Grünwald Giemsa staining captured with a Leica DM LB microscope with a ×40 objective. The cellularity and cellular composition of the granulocyte series are normal. C and D, Absence of erythroid precursor at ×100 magnification in the patient (Fig 1, D). E, Bone marrow mononuclear cells (15,000/well in duplicates) from a healthy adult control subject or the patient were cultured with Erythropoietin during 14 days. Erythroid progenitors (CFU-E and BFU-E) and granulocyte/macrophage progenitors (CFU-GM) were quantified. F and G, Bone marrow mononuclear cells from the patient and a healthy adult control subject were stained with anti-CD34 and anti-CD19 (Fig 1, F) or anti-CD34 and anti-IgM (gated on CD19+ cells; Fig 1, G). Numbers represent the percentage of cells within each quadrant or gate. Journal of Allergy and Clinical Immunology 2015 136, 1619-1626.e5DOI: (10.1016/j.jaci.2015.06.008) Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 2 Mutation identified in the catalytic domain of MYSM1. A, Pedigree of the patient's family. WGHM was performed with the subjects indicated by arrows. B, Direct sequencing of the MYSM1 gene in the patient and his parents. C, The mutation identified in the patient (p.H656R) is localized in the MPN domain and affects a histidine (H656 in red) highly conserved among species. D, Model of the 3-dimensional structure of the MYSM1 JAMM/MPN domain. E, Immunofluorescence with an anti-MYSM1 antibody revealed lower detection of MYSM1 in the patient's cells with that seen in a control subject. Identical parameters of image acquisition were applied in both conditions. Scale bars = 20 μm. F, Immunoblot of MYSM1 with lysates from a healthy control subject and the patient. KU70 and actin immunoblots were used as loading controls. Journal of Allergy and Clinical Immunology 2015 136, 1619-1626.e5DOI: (10.1016/j.jaci.2015.06.008) Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 3 Spontaneous genetic reversion in the patient. A, Immunohematologic values in the patient before (at 4 months) and after (at 33 and 39 months) reversion revealed a spontaneous correction to normal values in all immunohematopoietic cell compartments. Gray areas represent normal values obtained in healthy subjects. B, Sequencing analysis indicated that a spontaneous genetic reversion occurred in MYSM1 at position c.1967 in the patient's B lymphocytes, leading to a WT sequence on 1 allele. C, Quantitative analysis of WT (c.1967A) and mutated (c.1967G) MYSM1 sequences obtained by using high-throughput sequencing in the different subjects and cell types in patient at 39 months of age. D, Graphic representation of the results obtained in Fig 3, C. E, Analysis of bone marrow mononuclear cells from a healthy adult control subject and the patient after genetic reversion reveals complete restoration of B-cell development in the patient (compared with Fig 1, F). Journal of Allergy and Clinical Immunology 2015 136, 1619-1626.e5DOI: (10.1016/j.jaci.2015.06.008) Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 4 Frequency of reverted circulating PBMCs in the patient at 65 months of age. A, Quantitative analysis of WT (c.1967A) and mutated (c.1967G) MYSM1 sequences obtained by using high-throughput sequencing in the different subjects and cell types. B, Graphic representation of the results obtained in Fig 4, A. C, Graphic representation of the percentage of reverted cells in the different cell populations of the patient. Journal of Allergy and Clinical Immunology 2015 136, 1619-1626.e5DOI: (10.1016/j.jaci.2015.06.008) Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E1 Analysis of the T-cell receptor α (A) and β (B) repertoires in the patient at 28 months of age. cDNA prepared from PBMCs of the patient and a control subject was amplified in multiple PCRs primed by specific primers, followed by runoff reactions with a nested fluorescent primer specific for the segment. Labeled DNA copies were analyzed, and the size and intensity of each band were recorded and analyzed with Immunoscope software. CDR3 size distribution analysis of the patient's and control subject's peripheral T cells was performed for all AV and BV segments. Journal of Allergy and Clinical Immunology 2015 136, 1619-1626.e5DOI: (10.1016/j.jaci.2015.06.008) Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E2 Analysis of B-cell receptor IgM (A) and IgG (B) repertoires by using Immunoscope software in the patient at 39 months of age (after genetic reversion) and in a control subject reveals a polyclonal repertoire in the patient. Journal of Allergy and Clinical Immunology 2015 136, 1619-1626.e5DOI: (10.1016/j.jaci.2015.06.008) Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E3 The patient's circulating B cells are not of maternal origin. A, The patient's circulating B cells were enriched from PBMCs by means of magnetic cell sorting with an anti-CD19 antibody. B-cell enrichment was confirmed by using fluorescence-activated cell sorting analysis. B, Genetic study of the linkage patient's family. Two microsatellite repeats were amplified with fluorescently labeled primers. Then the alleles from each subject in the family were separated by size, and the marker was tested for linkage with another. The raw family data are represented. Colored arrows represent the different alleles. Circulating B lymphocytes in the patient are not of maternal origin because the microsatellite profiles from the mother's blood cells and the patient's B cells are different. Journal of Allergy and Clinical Immunology 2015 136, 1619-1626.e5DOI: (10.1016/j.jaci.2015.06.008) Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions