B-cell receptor profiling before and after IVIG monotherapy in newly diagnosed idiopathic inflammatory myopathies

Figures

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  Figure 1.. Identification of BcR clones in muscle tissues and peripheral blood before IVIG treatment. (A) Scatter plot of the BcR repertoire in muscle tissues and peripheral blood of IIM patients prior to IVIG treatment. Each dot represents a unique BcR clone. (B) Representative example of CDR3 clonal overlap between peripheral blood and muscle tissue pre-IVIG treatment, shown for patient one (Pt1). Each dot represents a unique BcR clone, and its frequency in the analysed repertoire is depicted on the x (blood pre-IVIG treatment) and y (muscle tissue pre-IVIG treatment) axes as percentage of total UMIs. The dotted lines on each axis indicate the 0.5% cut-off for dominant BcR clones. BcR clones in red are clones which are dominant in both samples. (C) Mutation load [expressed as mutations/base pair (bp)] of BcR clones detected in muscle tissues and peripheral blood prior to IVIG treatment. (D–F) Simpson’s index, Shannon entropy and Gini index to evaluate the diversity of the BcR repertoires in peripheral blood and muscle tissues at baseline

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  Figure 2.. BcR repertoire characteristics in peripheral blood before and after IVIG treatment. For each patient, panel (A) shows the number of dominant BcR clones while panel (B) shows the combined impact of all dominant BcR clones on the BcR repertoire before and 9 weeks after IVIG treatment. (C) Representative CDR3 overlap plot before (x-axis, dominant clones in green) and after (y-axis, dominant clones in red) IVIG treatment for one patient. Each dot represents a unique BcR clone, its frequency being calculated as percentage of total UMI-corrected reads. The dotted red lines on each axis indicate the 0.5% cut-off for dominant BcR clones. (D) A representative example of a CDR3 amino acid cluster analysis in one patient is shown. In red are newly formed dominant BcR clones 9 weeks after IVIG treatment. Clones present at baseline (in blue) show no clustering with the newly formed red clones. For clarity, only the top 100 clones at baseline are shown

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  Figure 3.. BcR repertoire in peripheral blood before and after IVIG treatment in responders and non-responders in peripheral blood. (A) The number of dominant BcR clones and (B) the impact of all dominant BcR clones before IVIG treatment. (C) the impact of all dominant BcR clones after IVIG treatment. *P < 0.05. Box plots show the median and 25th and 75th interquartile, error bars show the range. Single dots in grey represent values for each patient

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  Figure 4.. Correlation of BcR repertoire characteristics before and after treatment with markers of disease activity and therapy response. (A) The impact of all dominant BcR clones in blood at baseline vs CK levels at baseline. Correlation of the difference in impact of all dominant BcR clones in blood (week 9 minus week 0) with (B) the total improvement score (TIS) and (C) the improvement in manual muscle testing (MMT). P and r values are shown for each curve