Unsupervised clustering of human thymocyte subpopulations and leukemic cells. (A) Unsupervised classification of 11 subpopulations purified from normal human thymus and subsequently analyzed by global gene expression on the U133A array. For human thymic subsets, ETP indicates early thymocyte precursor with lymphomyeloid potential25,26 ; the Pro-T, Pre-T1, Pre-T2/Pre-T3(E) (ie, Pre-T2 and Pre-T3(E), not distinguished here), Pre-T3(L), immature DP (immature double-positive cells), DP-TCRαβlo, DP-TCRαβint and DP-TCRαβbr, CD4-SP (CD4 single-positive cells), and CD8-SP, have been described previously (for a review, see Carrasco et al4 ). The lineage choice, β-selection, and selection processes as reported in normal thymus differentiation are indicated. The 469 probe sets differentially expressed between oncogenic groups (Figure 4A) were filtered for variable and reliable thymic expression. In addition, “proliferation genes” defined by the “proliferation-mitosis” cluster (cluster C6 in Figure 4A) were discarded from this analysis to avoid spurious sample clustering due to proliferation rate. The resulting final list of 168 “thymic” genes is shown in Table S3. Genes of particular interest are shown, and HOXA genes are indicated in red. (B) Unsupervised classification of T-ALL samples using the same 168 “thymic” gene list. The same conventions are used as in Figure 2. The main oncogenic subgroups are indicated. The same genes of interest as in Figure 5A are shown. (C) Unsupervised analysis of combined T-ALL samples, normal human thymic subpopulations, and bone marrow (BM) cells. A selection of genes with a strongly altered expression level compared with the corresponding normal thymic subsets is indicated (RAG1 and CD8A gene expression was also directly analyzed by RQ-PCR in normal thymic samples and T-ALL, giving consistent data; not shown). (D) Three-dimensional representation of a multidimensional scaling analysis performed using normal thymic subsets, normal bone marrow, and T-ALL samples of the main oncogenic subgroups (TAL_RA, TAL_RB, HOXA, TLX1, TLX3, immature). The lineage choice, β-selection, and selection processes are indicated.
