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V. Giudice et al.
CDR3 size and DJ length profiles were defined in total CD4+ and CD8+ cells and compared within each patient (Figure 4B and Online Supplementary Figure S8B). In CD4+ cells, all patients displayed CDR3 profiles with normal Gaussian distribution, as described in healthy subjects. In CD8+ cells, Patients AA7, AA8, and AA10 to AA12 had CDR3 size profiles with Gaussian distributions. In the
remaining patients, CDR3 profiles showed different shapes with 8-13 different classes and 1 or 2 predomi- nant peaks of various nt sizes (36-57). For DJ length pro- files in SAA patients, the asymmetric Gaussian distribu- tion was described in all CD4+ cells, and in 6 (AA5-AA8 and AA11-AA12) CD8+ populations. Similarly, TRBV/TRBJ rearrangement plots from the CD8+CD57+
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Figure 6. Homology assessment. (A) CDR3 sequence pools were analyzed among patients (AA) and healthy subjects (HC) for the presence of homology. Shared and immunodominant sequences were reported as a heatmap based on their relative expression: in the same row, from lowest (gray; <0.01%) to highest (red; >5%) val- ues. (B) Structural analysis was performed comparing the sequences for common pattern, using both alignments at the N-terminal of Vβ gene (left) or at the C-ter- minal of Jβ gene (right).
haematologica | 2018; 103(5)