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1.
Figure 1

Figure 1. Unsupervised hierarchical clustering of PTCL/U, AITL, and ALCL.. From: Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets.

Unsupervised analysis performed on 28 PTCL/U, 6 AITL, and 6 ALCL samples. The 40 samples are clustered according to the expression of 417 genes. While ALCLs roughly cluster together, AITLs are scattered within PTCL/U.

Pier Paolo Piccaluga, et al. J Clin Invest. 2007 March 1;117(3):823-834.
2.
Figure 5

Figure 5. Cellular programs deregulated in PTCL/U.. From: Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets.

Fifty-seven of the 155 genes found to be differentially expressed in PTCL/U and normal T lymphocytes could be classified according to 7 functional categories known to be particularly relevant to malignant behavior. Gene names are indicated. For description of the matrix, see the legend to Figure 4.

Pier Paolo Piccaluga, et al. J Clin Invest. 2007 March 1;117(3):823-834.
3.
Figure 6

Figure 6. Immunohistochemical validation of gene expression results on TMAs.. From: Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets.

Examples of the immunostaining patterns for PDGFRα (A), p-PDGFRα (B), CYR61 (C), BCL10 (D), IGFBP7 (E), LIFR (F), p27 (G), and caldesmon (H). The insets show the staining for the corresponding marker in normal lymphoid tissue (F, follicle; P, paracortex/T zone). Original magnification, ×400.

Pier Paolo Piccaluga, et al. J Clin Invest. 2007 March 1;117(3):823-834.
4.
Figure 2

Figure 2. Relatedness of PTCL/U to resting and activated normal lymphocytes.. From: Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets.

Relatedness of the gene expression profile of PTCL/U to normal T cell populations. (A) A supervised analysis was used to identify the genes differentially expressed between 2 groups of samples. HLA-DR+ (activated) T cells are compared with HLA-DR (resting) T cells. The expression of the selected genes is investigated in PTCLs/U, represented on the right side of the matrix. (B) A cell-type classification is used to measure the relatedness of PTCL/U to HLA-DR+ and HLA-DR T cells. The gray area marks 95% confidence: the P value decreases with increasing distance from the x axis.

Pier Paolo Piccaluga, et al. J Clin Invest. 2007 March 1;117(3):823-834.
5.
Figure 8

Figure 8. ITF2357 reduces PTCL/U primary cells’ viability ex vivo.. From: Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets.

(A) PTCL/U and normal T cells were incubated for 48 hours in media containing 10% FBS with or without ITF2357 at concentrations of 0.5, 1, and 5 μM. ITF2357 induced concentration-dependent growth inhibition of PTCL/U primary cells with a scarce effect on normal T lymphocyte viability. The results are plotted as the percentage of control untreated cells. Bars indicate the SEM of triplicate samples. (B and C) This effect was consistent with the G0/G1 cell cycle arrest and apoptosis induction.

Pier Paolo Piccaluga, et al. J Clin Invest. 2007 March 1;117(3):823-834.
6.
Figure 3

Figure 3. Relatedness of PTCL/U to CD4 and CD8 normal lymphocytes.. From: Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets.

Relatedness of the gene expression profile of PTCL/U to normal T cell populations. A supervised analysis was used to identify the genes differentially expressed between 2 groups of samples. (A) CD4+ T cells are compared with CD8+ T cells. The expression of the selected genes is investigated in PTCLs/U, represented on the right side of the matrix. (B) A cell-type classification is used to measure the relatedness of PTCL/U to CD4+ and CD8+ T cells. The gray area marks 95% confidence: the P value decreases with increasing distance from the x axis.

Pier Paolo Piccaluga, et al. J Clin Invest. 2007 March 1;117(3):823-834.
7.
Figure 7

Figure 7. Imatinib mesylate reduces PTCL/U primary cells' viability ex vivo.. From: Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets.

(A) PTCL/U and normal T cells were incubated for 48 hours in media containing 10% FBS with or without imatinib at concentrations of 1, 5, and 10 μM. Imatinib induced concentration-dependent growth inhibition of PTCL/U primary cells with a very scarce effect on normal T lymphocyte viability. The results are plotted as the percentage of control untreated cells. Bars indicate the SEM of triplicate samples. (B and C) This effect was consistent with the G0/G1 cell cycle arrest and apoptosis induction.

Pier Paolo Piccaluga, et al. J Clin Invest. 2007 March 1;117(3):823-834.
8.
Figure 4

Figure 4. Supervised analysis of PTCL/U and normal lymphocytes identifies differentially expressed genes.. From: Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets.

Identification of genes differentially expressed in PTCL/U and normal T lymphocytes. Supervised analysis was performed using 17 samples of PTCL/U (training set) versus the 3 normal T cell subpopulations identified as the closest normal counterparts (CD4+, CD8+, and HLA-DR+). The support value for the analysis was chosen as n = n0 (n0, number of samples in the phenotype set). (A) The analysis identified 155 genes that are differentially expressed in PTCL/U versus all the other samples (Supplemental Tables 5 and 6). The expression of the 155 genes was then investigated and validated in an independent test set (11 PTCL/U cases), represented on the right side of the matrix. (B) A cell-type classification is used to measure the relatedness of test set cases to PTCL/U (training set) and normal T cells. The gray area marks 95% of confidence: the P value decreases with increasing distance from the x axis. (C) In addition, the identified 155 genes correctly classified all the 11 PTCLs/U of the test set in unsupervised analysis.

Pier Paolo Piccaluga, et al. J Clin Invest. 2007 March 1;117(3):823-834.

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