Additional file 2 of Immunological and genetic kinetics from diagnosis to clinical progression in chronic lymphocytic leukemia

Additional file 2: Supplementary Table S1. Monoclonal antibodies (mAbs). Supplementary Table S7. Highlighted dysregulated genes in T CLL cells at progression. Supplementary Figure S1. Longitudinal analysis of the CCF of CNVs from paired B-CLL cells at diagnosis and progression before treatment. Comparison of the CCF with 95% CI for each CNV detected per patient (n = 10) between diagnosis and progression. Significantly increased (red lines) and stable CCF (grey lines) are shown. Recurrent CNVs in CLL (del(13q), del(11q), del(17p) and +[12]) are plotted with bold lines and labeled with CNV name: stable CCF (bold black) is shown. Supplementary Figure S2. CD8+ T cell differentiation subsets and PD1 expression in CD8+ T cells from progressing and non-progressing CLL patients. a CD4/CD8 ratio in progressing (n = 19) and non-progressing patients (n = 10) at diagnosis and progression or non-progression. b Absolute numbers of CD8+ T cell differentiation subsets (naive: CCR7+CD45RA+; central memory, CM: CCR7+CD45RA−; effector memory, EM: CCR7−CD45RA− and EM CD45RA+, EMRA: CCR7−CD45RA+) in progressing (n = 19) and non-progressing patients (n = 10) at diagnosis and progression or non-progression. c Absolute numbers of PD1+CD8+ T cells in progressing (left, n = 19) and non-progressing patients (middle, n = 10) at diagnosis and progression or non-progression. Fold change of PD1+CD8+ T cells between time points comparing progressing and non-progressing patients (right). d Percentage of PD1+CD244+ CD8+ T cells in progressing (left, n = 12) and non-progressing patients (middle, n = 9) at diagnosis and progression or non-progression. Fold change of PD1+CD244+CD8+ T cells between time points comparing progressing and non-progressing patients (right). e Percentage of PD1+ 160+ CD8+ T cells in progressing (left, n = 12) and non-progressing patients (middle, n = 9) at diagnosis and progression or non-progression. Fold change of PD1+CD160+CD8+ T cells between time points comparing progressing and non-progressing patients (right). f Density plots of PD1, CD160 and CD244 coexpression in CD8+ T cells in representative patients at diagnosis and progression and at diagnosis and non-progression. Graphs show mean ± SEM or paired values (*P < 0.05; **P < 0.01; ***P < 0.001; Wilcoxon matched paired test or Mann-Whitney test). Supplementary Figure S3. Flow cytometric analysis of progenitor and terminal CD8+ subsets. Gating strategy followed for the identification of T-bethiEomesdim/−PD1mid and T-betdim/−EomeshiPD1hi CD8+ populations. Supplementary Figure S4. Co-expression of PD1 and CD244 in CD8+ T cells after co-culture with B-CLL cells. MDSCs in progressing and non-progressing CLL patients. a Percentages of PD1+CD244+ cells out of CD8+ T cells from progressing (left) and non-progressing (right) CLL patients after stimulation with anti-CD3 and anti-CD28 for 7 days (grey dots) and in presence of B-HD cells (yellow dots) or B-CLL cells at the time of progression (red dots, n = 10) or asymptomatic follow-up (blue dots, n = 7) at the indicated T:B ratios. b Percentages of PD1+CD244+ cells out of CD8+ T cells from healthy age-matched donors (T-HD) after stimulation with anti-CD3 and anti-CD28 for 7 days (grey dots) and in presence of B-CLL cells at progression (bold red dots) or B-CLL cells at asymptomatic follow-up (bold blue dots) at the indicated T:B ratios. c Percentages of CD8+ T cells from CLL patients co-expressing PD1 and CD244 after stimulation with anti-CD3 and anti-CD28 for 7 days and in contact with B-CLL cells or separated by transwell inserts at 1:10 T:B ratio for 7 days (n = 14).d Dot plots of IL-10+ B cells gated on CD19+CD5+ cells after 5 h of leukocyte stimulation (PIB), or brefeldin A (BFA) as control, from one representative patient from the progressed and non-progressed groups respectively. e Percentage of MDSCs (CD14+HLA-DRlow/−) out of CD14+ cells in progressing (left, n = 17) and non-progressing patients (middle, n = 10) at diagnosis and progression or non-progression. Increment of MDSCs between time points comparing progressing and non-progressing patients (right). Graphs show mean ± SEM or paired values (*P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001; Wilcoxon matched paired test or Mann-Whitney test).