RASGRP1 mutation in autoimmune lymphoproliferative syndrome-like disease Huawei Mao, MD, PhD, Wanling Yang, PhD, Sylvain Latour, PhD, Jing Yang, PhD,

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RASGRP1 mutation in autoimmune lymphoproliferative syndrome-like disease Huawei Mao, MD, PhD, Wanling Yang, PhD, Sylvain Latour, PhD, Jing Yang, PhD, Sarah Winter, PhD, Jian Zheng, PhD, Ke Ni, MPhil, Minmin Lv, MPhil, Chenjing Liu, MPhil, Hongmei Huang, MD, Koon-Wing Chan, MPhil, Pamela Pui-Wah Lee, MD, Wenwei Tu, PhD, Alain Fischer, MD, PhD, Yu-Lung Lau, MD Journal of Allergy and Clinical Immunology Volume 142, Issue 2, Pages 595-604.e16 (August 2018) DOI: 10.1016/j.jaci.2017.10.026 Copyright © 2017 The Authors Terms and Conditions

Fig 1 The family pedigree and phenotype of the patients. A, The pedigree of the family and the RASGRP1 genotypes are shown. WT denotes wild type. B and C, Computed tomography demonstrated hepatosplenomegaly and mediastinal (triangle) and superficial cervical (arrow) lymphadenopathy in the sister. TCRαβ+ DNT cells (D) and CD21low B cells (E) in the PBMCs were examined by flow cytometry. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig 2 Novel compound heterozygous mutations in RASGRP1 were identified in the patients. A, Compound heterozygous mutations in both patients and heterozygous carrier in the parents were shown in genomic RASGRP1 DNA. B, The schematic structure of RasGRP1. The mutations are located in the Cdc25 domain. C, Phylogenetic analysis indicated that the positions of mutations are highly conserved across different species. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig 3 Normal RasGRP1 expression, but impaired ERK activation, in patient cells. A, RasGRP1 protein expression in lymphocytes was examined by flow cytometry. Both patients had comparable level of RasGRP1 protein with normal controls. B, PMA-induced ERK activation in lymphocytes was examined by flow cytometry. Both patients had markedly lower phosphorylation of ERK compared with normal controls. pERK, Phosphorylated ERK Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig 4 Impaired activation and proliferation in patient T cells. A, PBMCs were stimulated with anti-CD3 and anti-CD28 antibodies overnight. The percentage of CD69-positive cells in lymphocytes and intensity of CD69 expression level (right upper corner) were examined by flow cytometry. B, PBMCs were stimulated with anti-CD3 and anti-CD28 antibodies, and lymphocyte proliferation was examined by CFSE dilution. CFSE, Carboxyfluorescein succinimidyl ester. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig 5 Impaired activation-induced cell death in patient T cells. A, After stimulation with anti-CD3 and anti-CD28 antibodies, intracellular expression of active caspase 3 in lymphocytes was examined. B, PBMCs were stimulated with PMA and ionomycin. Lymphocyte apoptosis was examined using annexin V and propidium iodide staining. C, PBMCs were stimulated with anti-CD3 and anti-CD28 antibodies. IL-10 production in the supernatants was examined. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E1 TCRαβ+ and TCRγδ+ T cells in the patients. The PBMCs were stained for the surface expressions of TCRαβ and TCRγδ. The percentage of CD3+TCRαβ+ and CD3+TCRγδ+ T cells out of total CD3+ T cells was determined by flow cytometry. The patient showed reduced expression of TCRαβ, but largely elevated expression of TCRγδ. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E2 Examination of Treg cells in the patients. The PBMCs were stained for the surface expressions of CD3 and CD4, and intracellular expression of Foxp3. The percentage of Foxp3+ Treg cells out of CD4+ T cells was determined by flow cytometry. Treg, Regulatory T. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E3 The phenotype of B cells in the patients. The PBMCs were stained for the surface expressions of CD3, CD19, CD27, and IgD. The percentages of naive B cells (CD3−CD19+CD27−IgD+), nonswitched B cells (CD3−CD19+CD27+IgD+), and switched B cells (CD3−CD19+CD27+IgD−) were determined by flow cytometry. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E4 Alignment of sequencing reads around the 2 mutations in RASGRP1. This was performed by IGV (Integrative Genomics Viewer) of the raw sequencing reads in the reverse strand. Codon ACC (Thr) was mutated to ATC (Ile) in the father and the 2 affected siblings. Codon AAG (Lys, K) was mutated to TAG (stop codon) in the mother and the 2 siblings. Shown in the IGV are reverse sequences. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E5 Structure analysis of the mutant RasGRP1. The structural impact of variant Thr214Ile was analyzed on the basis of template of 4L9M from PDB. The residue 214 together with certain nearby residues within 6 Å was illustrated in the wild-type (WT) and variant RasGRP1 by Swiss-PdbViewer. Computed hydrogen bonds are shown as green dashed lines. Residues Thr214/Ile214 are highlighted in pink. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E6 Normal RasGRP1 expression in T and B cells of the patients. The PBMCs were stained first for the surface expressions of CD3 and CD19, and then fixed, permeabilized, and labeled with anti-RasGRP1 antibody. The expression of RasaGRP1 in CD3+ T (A) and CD19+ B (B) cells was examined by flow cytometry. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E7 PMA-induced ERK activation was impaired in patient T cells, but not in B cells. PBMCs were stimulated with PMA for 5 minutes. Phosphorylated ERK (pERK) expression was examined by flow cytometry in CD4+ (A), C8+ (B) T, and CD19+ B (C) cells. The increase in the percentage of pERK expression in stimulated cells relative to resting cells was calculated. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E8 TCR stimulation-induced T-cell activation was impaired in the patients. The PBMCs were stimulated with anti-CD3 and anti-CD28 antibodies overnight. The percentage of CD69-positive cells out of CD4+ (A) and C8+ (B) T cells was examined by flow cytometry. The mean fluorescence intensity of CD69 expression was indicated at the right upper corner of each histogram. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E9 CFSE dilution test showed the impaired TCR-stimulated T-cell proliferation in the patients. The PBMCs were first stained with 1 mM CFSE, and then stimulated with anti-CD3 and anti-CD28 antibodies for 4 days. The proliferation of CD4+ (A) and C8+ (B) T cells was examined by flow cytometry. CFSE, Carboxyfluorescein succinimidyl ester. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E10 TCR stimulation-induced T-cell proliferation was impaired in the patients. The PBMCs were stimulated with LEAF-purified anti-CD3 and anti-CD28 antibodies for 2 days. The intracellular expression of Ki67 in CD4+ (A) and C8+ (B) T cells was examined by flow cytometry. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E11 Transfection of T cells by RasGRP1-expressing lentivirus. T cells of normal control and patient were transfected with the lentivirus expressing wild- type RasGRP1 and mCherry. The mCherry expression in T cells was examined by flow cytometry. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions

Fig E12 Impaired activation-induced cell death in patient T cells. The PBMCs were stimulated with LEAF-purified anti-CD3 and anti-CD28 antibodies for 2 days. The intracellular expression of active caspase 3 in CD4+ (A) and C8+ (B) T cells was examined by flow cytometry. Journal of Allergy and Clinical Immunology 2018 142, 595-604.e16DOI: (10.1016/j.jaci.2017.10.026) Copyright © 2017 The Authors Terms and Conditions