Additional file 1: of Monocyte-derived tissue transglutaminase in multiple sclerosis patients: reflecting an anti-inflammatory status and function of the cells?

TG2 expression in untreated and drug-treated MS patients. qPCR analysis was performed to detect TG2 in primary human monocytes isolated from untreated (N = 10) and drug-treated (N = 5) MS patients. Data are shown in box-and-whisker plots in which the median is represented by the horizontal line within the box, and the lower and upper whiskers represent the 5 and 95 percentiles. (TIFF 1769 kb

Additional file 2 of Extended interval dosing of ocrelizumab modifies the repopulation of B cells without altering the clinical efficacy in multiple sclerosis

Additional file 2: Table S1. Median expression of markers. Table S2. Mean and standard deviation of the percentage of each immune cell subset. Table S3. Mean and standard deviation of the percentage of each B cell subset among all CD19+ cells. Table S4. Median expression markers of migratory markers. Table S5. Median expression markers of migratory markers. Table S6. Mean and standard deviation of the percentage of each B cell subset among all CD45+ cells with follow-up sample. Table S7. Statistics of Δ. Table S8. Mean and standard deviation of the percentage of each B cell subset among all CD45+ cells with follow-up sample in GC patients

Additional file 1 of Extended interval dosing of ocrelizumab modifies the repopulation of B cells without altering the clinical efficacy in multiple sclerosis

Additional file 1: Figure S1. Pre-gating strategy of the CyTOF. A. Representation of dotplots of the pre-gating strategy of the data obtained with the CyTOF. (1) Removal of cell debris, beads and doublets, (2) cleaning signal over time with flowCut, (3) debarcoding, (4) selection of CD45+ live cells and (5) batch normalization with CytoNorm. B. Dotplot represents the pre-gating of CD3+CD19−, CD3−CD19+ and CD3−CD19− cells for further analysis. Figure S2. B cell subclustering. A. Heatmap displays the median scaled intensities of all the markers across the annotated B cell subclusters. B. Bar plots of the percentage of each annotated B cell subpopulation out of the total CD19+ cells from CG, SID and EID patients. Each data point corresponds to each individual, columns and error bars show mean ± SEM. P-values indicate the statistical differences after a GLM model with age, sex and type of MS as covariates. *adjusted p-value < 0.05, **adjusted p-value < 0.01, ***adjusted p-value < 0.001, ****adjusted p-value < 0.0001. GLM = multivariate general linear model; CG = control group; SID = standard interval dosing; EID = extended interval dosing. Figure S3. T cell and rest of immune cell subclustering. A. Heatmap shows the median scaled intensities of all the markers across the annotated T cell subclusters. B. Heatmap represents the median scaled intensities of all the markers across the annotated CD3−CD19− cell subclusters. Th = T helper cells; Tregs = regulatory T cells; Temra = T effector memory re-expressing CD45RA cells; NKT = natural killer T cells; DN = double negative; DP = double positive cells; NK = natural killer cells. Figure S4. Longitudinal cohort after treatment with standard or extended interval dosing of ocrelizumab. A. Bar plots display the percentage of annotated B cell subsets out of the total CD45 + cells from patients that went from SID to SID, SID to EID, EID to SID and EID to EID. B. Violin plots display the Δ or subtraction of the percentage of annotated B cell subsets out of the total CD45+ cells at the second blood sampling minus the percentage of annotated B cell subsets out of the total CD45+ cells at the first blood sampling. P-values indicate the statistical differences after a GLM model of the change of percentages between groups of patients, with age, sex and type of MS as covariates. C. Schematic overview of the longitudinal study design and timeline for CG patients. D. Percentage of annotated B cell subsets out of the total amount of CD45+ cells from patients that went from CG to SID and CG to EID. A and D. Each data point corresponds to each individual, columns and error bars show mean ± SEM. P-values indicate the statistical differences after a GLMM model with age, sex and type of MS as covariates and patient ID as a random effect. *adjusted p-value < 0.05, **adjusted p-value < 0.01, ***adjusted p-value < 0.001, ****adjusted p-value < 0.0001; #unadjusted p-value < 0.05. OCR = ocrelizumab; GLM = multivariate general linear model; GLMM = multivariate general linear mixed model; CG = control group; SID = standard interval dosing; EID = extended interval dosing; T1 = first-time point/blood sampling; T2 = second-time point/blood sampling

Additional file 1: Table S1. of Physiological evidence for diversification of IFNι- and IFNβ-mediated response programs in different autoimmune diseases

List of 23 type I interferon (IFN) response genes that were measured. Table S2. List of genes that are significantly differentially expressed between patients with systemic lupus erythematosus (SLE) and patients with multiple sclerosis (MS) who were treated with IFNβ. (PDF 116 kb