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Blood, Vol. 110, Issue 10, 3706-3714, November 15, 2007
Distinct gene expression profiles of acute myeloid/T-lymphoid leukemia with silenced CEBPA and mutations in NOTCH1
Blood Wouters et al.
110: 3706
Supplemental materials for: Wouters et al
Files in this Data Supplement:
- Document 1. Supplemental materials and methods (PDF, 83.6 KB)
- Table S1. Characteristics and CEBPA mutations of AML patients in GEP cluster #4 (PDF, 75.4 KB)
- Table S2 (PDF, 273 KB) -
A. Genes differentially upregulated in GEP cluster #4 AML cases with silenced CEBPA compared to GEP cluster #4 cases with CEBPA mutation.
B. Genes differentially downregulated in GEP cluster #4 AML cases with silenced CEBPA compared to GEP cluster #4 AML cases with CEBPA mutation.
- Table S3 (PDF, 62.8 KB) -
A. CEBPA expression levels and CEBPA promoter methylation.
B. Control AML samples analyzed for NOTCH1 mutations by direct sequencing and/or dHPLC and for CEBPA promoter hypermethylation.
C. Additional control AML samples analyzed for NOTCH1 mutations by dHPLC.
- Table S4. Array expression levels of a selection of genes with significantly elevated expression levels in GEP cluster #4 AML cases: cases with CEBPA mutation versus cases with silenced CEBPA (PDF, 35.9 KB)
- Table S5. Functional networks of genes, differentially expressed in GEP cluster #4 AML cases with silenced CEBPA, obtained by Ingenuity pathways analysis (PDF, 105 KB)
- Table S6. Morphology, cytogenetics and selected immunophenotype of AML cases predicted by a 9 probe set gene expression prediction signature in an independent cohort of 268 patients (PDF, 35.5 KB)
- Table S7. Clinical outcome of patients identified in first cohort of AML and 4 patients with same characteristics identified in second cohort of AML (PDF, 32.6 KB)
- Figure S1. Ingenuity pathways analysis of genes differentially upregulated in cluster #4 cases without CEBPA mutations (JPG, 102 KB)
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Probe sets for all genes significantly higher expressed in cluster #4 cases without CEBPA mutations compared to cluster #4 cases with CEBPA mutations (Table S2) were loaded into Ingenuity Pathways Analysis software. Each probe set was mapped to its corresponding gene object in the Ingenuity Pathways Knowledge Base. These genes, called focus genes, were overlaid onto a global molecular network developed from information contained in the Ingenuity Pathways Knowledge Base. Networks of these focus genes were then algorithmically generated based on their connectivity. The figure displayed represents the network with the highest score (see also Table S5), and is highly associated with T-cell development. The network in this figure is a graphical representation of the molecular relationships between genes/gene products. Genes or gene products are represented as nodes, and the biological relationship between two nodes is represented as an edge (line). The intensity of the node red color indicates the degree of upregulation. Nodes are displayed using various shapes that represent the functional class of the gene product. Genes associated with biological functions and/or diseases in the Ingenuity Pathways Knowledge Base were considered for functional analysis of the network. Top biological functions of genes in this network as indicated by Ingenuity are cellular development, hematological development and function, and immune and lymphatic system development and function. See Table S5 for more details and additional functional networks. In some cases gene names indicated by Ingenuity differ from names used in Affymetrix annotation of probe sets, e.g. CD247 is identical to CD3Z.
- Figure S2. Activated NOTCH1 upregulates TRIB2 in U937 cells (JPG, 12.6 KB)
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Human U937 leukemia cells were transduced with empty virus (MigR1) or ICN1 according to methods as described in Materials and Methods. Cells were sorted for GFP expression and mRNA was isolated. HES1 (left panel) and TRIB2 (right panel) expression was assessed by RQ-PCR. Data are representative of the mean +/− standard deviation of 3 independent experiments performed in duplicate. PCR primers for human TRIB2 were previously described in reference 15 of the main text, and primers for human HES1 were: 5′-ATGGAGAAAAATTCCTCGTCCC-3′ (forward) and 5′-TTCAGAGCATCCAAAATCAGTGT-3′ (reverse).
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