Limits...
Five distinct biological processes and 14 differentially expressed genes characterize TEL/AML1-positive leukemia.

Gandemer V, Rio AG, de Tayrac M, Sibut V, Mottier S, Ly Sunnaram B, Henry C, Monnier A, Berthou C, Le Gall E, Le Treut A, Schmitt C, Le Gall JY, Mosser J, Galibert MD - BMC Genomics (2007)

Bottom Line: We compared the leukemia cell gene expression profiles of 16 TEL/AML1-positive ALL patients to those of 44 TEL/AML1-negative patients, whose blast cells did not contain any additional recurrent translocation.These results were first confirmed by the analysis of an additional microarray data-set (7 patient samples) and second by real-time RT-PCR quantification and clustering using an independent set (27 patient samples).Gene expression analyses of leukemia cells from 60 children with TEL/AML1-positive and -negative B-lineage ALL led to the identification of five biological processes, associated with 14 validated genes characterizing and highlighting the biology of the TEL/AML1-positive ALL sub-group.

View Article: PubMed Central - HTML - PubMed

Affiliation: CNRS UMR 6061 Laboratoire de Génétique et Développement, Equipe Régulation transcriptionnelle et oncogenèse, Université de Rennes-1, Faculté de Médecine, IFR140 GFAS, 2 av du Pr Léon Bernard, CS 34317, Rennes cedex, France. virginie.gandemer@chu-rennes.fr

ABSTRACT

Background: The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of ETV6 (TEL) and RUNX1 (AML1) genes and defines a relatively uniform category, although only some patients suffer very late relapse. TEL/AML1-positive patients are thus an interesting subgroup to study, and such studies should elucidate the biological processes underlying TEL/AML1 pathogenesis. We report an analysis of gene expression in 60 children with B-lineage ALL using Agilent whole genome oligo-chips (44K-G4112A) and/or real time RT-PCR.

Results: We compared the leukemia cell gene expression profiles of 16 TEL/AML1-positive ALL patients to those of 44 TEL/AML1-negative patients, whose blast cells did not contain any additional recurrent translocation. Microarray analyses of 26 samples allowed the identification of genes differentially expressed between the TEL/AML1-positive and negative ALL groups. Gene enrichment analysis defined five enriched GO categories: cell differentiation, cell proliferation, apoptosis, cell motility and response to wounding, associated with 14 genes -RUNX1, TCFL5, TNFRSF7, CBFA2T3, CD9, SCARB1, TP53INP1, ACVR1C, PIK3C3, EGFL7, SEMA6A, CTGF, LSP1, TFPI - highlighting the biology of the TEL/AML1 sub-group. These results were first confirmed by the analysis of an additional microarray data-set (7 patient samples) and second by real-time RT-PCR quantification and clustering using an independent set (27 patient samples). Over-expression of RUNX1 (AML1) was further investigated and in one third of the patients correlated with cytogenetic findings.

Conclusion: Gene expression analyses of leukemia cells from 60 children with TEL/AML1-positive and -negative B-lineage ALL led to the identification of five biological processes, associated with 14 validated genes characterizing and highlighting the biology of the TEL/AML1-positive ALL sub-group.

Show MeSH

Related in: MedlinePlus

Analysis flowchart: overview of the strategy used for gene selection using Set-A microarray data. At each level, the data set was filtered to remove genes that showed poor robustness and no significant difference in expression level between the TEL/AML1-positive and the TEL/AML1-negative ALL subclasses. SAM denotes Significant Analysis of Microarrays. Two groups of genes (according to the filters applied) were selected and functionally annotated. Nine of the 16 genes were selected for RT-PCR validation on the basis of their biological relevance.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2211320&req=5

Figure 1: Analysis flowchart: overview of the strategy used for gene selection using Set-A microarray data. At each level, the data set was filtered to remove genes that showed poor robustness and no significant difference in expression level between the TEL/AML1-positive and the TEL/AML1-negative ALL subclasses. SAM denotes Significant Analysis of Microarrays. Two groups of genes (according to the filters applied) were selected and functionally annotated. Nine of the 16 genes were selected for RT-PCR validation on the basis of their biological relevance.

Mentions: To identify genes with expression profiles that differentiate TEL/AML1-positive patients from TEL/AML1-negative patients with no recurrent chromosomal abnormalities we used data Set-A. We selected 10761 gene signals that displayed log-ratio intensities that were significantly different from the mean (PvalueLogRatio < 0.01) for at least one array. Only 10416 gene signals, those present on at least 70% of the Set-A arrays, were retained for SAM analysis. Two preliminary two-class SAM were performed, comparing TEL/AML1-positive patient data to either TEL/AML1-negative HR or SR patient data to assess specific sample behavior in a more homogeneous situation than the pooled TEL/AML1-negative HR and SR group [16]. Interestingly, we found that patient 18, the only TEL/AML1-positive HR patient (who was initially excluded from SAM analysis because he belonged to both groups) segregated with the TEL/AML1-positive SR group and not with the HR patient group. This is consistent with the fusion transcript affecting the gene expression profile (data not shown). Similarly, we found that patient 9, a TEL/AML1-negative patient, clustered within the TEL/AML1 branch and that patient 17, a TEL/AML1-postive patient, did not segregate into the TEL/AML1 branch. RT-PCR, using a different set of primers in a different laboratory, confirmed the presence of a TEL/AML1 transcript in patient 17 and its absence from patient 9; this indicates some heterogeneity in the TEL/AML1 group (data not shown). To avoid heterogeneity bias associated with particular patients and to highlight general processes, patients 9 and 17 were withdrawn from the two-class SAM gene-selection step comparing the TEL/AML1-positive group with the TEL/AML1-negative group. However, the data for these two patients were included in the final HC representation. To increase the robustness of gene-selection step, two cut-offs were applied successively, consistent with a 1.7-fold change, to exclude genes that varied little between the samples, (FC > 1.7), with or without a Q-value filter (Qvalue < 0.02) limiting the number of genes selected (Figure 1). This gave two TEL/AML1 gene sets, one of 181 genes and the other of 103 genes. These gene sets were used for hierarchical clustering representation of patient Set-A. Because the Set-A cohort was small, we validated our second selection (181 genes) by estimating the Benjamini and Hochberg false discovery rate (FDR): this value was consistently low (3.19% indicating only six false positives among the 181 genes designated as significant, data not shown). Both gene sets (181; 103) were able to cluster the TEL/AML1-positive Set-A patients, other than patients 9 and 17, in one branch. Hierarchical clustering highlighted 74 distinct genes among the 181 selected and they were separated into two clusters (data not shown). With the group of 103 selected genes, hierarchical clustering highlighted two clusters (44 distinct genes) able to group TEL/AML1-positive ALL (each cluster corresponds to a single branch of the hierarchical tree in which intercluster distance directly correlates with dissimilarity in gene expression) (Figure 2A). A resampling-based procedure (bootsrapping) was used to assess reproducibility (data not shown). Only these two restricted gene sets, of 74 and 44 genes, which correspond to a different profile of expression behavior associated with the presence of a TEL/AML1 chromosomal rearrangement, were able on their own to cluster the TEL/AML1 Set-A patients as previously and the TEL/AML1 Set-B patients into one branch. They were also able to segregate, with 100% reproducibility, the TEL/AML1 Set-A and -B patients together in the same branch, with the exceptions of patients 9 and 17 (Figure 2B).


Five distinct biological processes and 14 differentially expressed genes characterize TEL/AML1-positive leukemia.

Gandemer V, Rio AG, de Tayrac M, Sibut V, Mottier S, Ly Sunnaram B, Henry C, Monnier A, Berthou C, Le Gall E, Le Treut A, Schmitt C, Le Gall JY, Mosser J, Galibert MD - BMC Genomics (2007)

Analysis flowchart: overview of the strategy used for gene selection using Set-A microarray data. At each level, the data set was filtered to remove genes that showed poor robustness and no significant difference in expression level between the TEL/AML1-positive and the TEL/AML1-negative ALL subclasses. SAM denotes Significant Analysis of Microarrays. Two groups of genes (according to the filters applied) were selected and functionally annotated. Nine of the 16 genes were selected for RT-PCR validation on the basis of their biological relevance.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2211320&req=5

Figure 1: Analysis flowchart: overview of the strategy used for gene selection using Set-A microarray data. At each level, the data set was filtered to remove genes that showed poor robustness and no significant difference in expression level between the TEL/AML1-positive and the TEL/AML1-negative ALL subclasses. SAM denotes Significant Analysis of Microarrays. Two groups of genes (according to the filters applied) were selected and functionally annotated. Nine of the 16 genes were selected for RT-PCR validation on the basis of their biological relevance.
Mentions: To identify genes with expression profiles that differentiate TEL/AML1-positive patients from TEL/AML1-negative patients with no recurrent chromosomal abnormalities we used data Set-A. We selected 10761 gene signals that displayed log-ratio intensities that were significantly different from the mean (PvalueLogRatio < 0.01) for at least one array. Only 10416 gene signals, those present on at least 70% of the Set-A arrays, were retained for SAM analysis. Two preliminary two-class SAM were performed, comparing TEL/AML1-positive patient data to either TEL/AML1-negative HR or SR patient data to assess specific sample behavior in a more homogeneous situation than the pooled TEL/AML1-negative HR and SR group [16]. Interestingly, we found that patient 18, the only TEL/AML1-positive HR patient (who was initially excluded from SAM analysis because he belonged to both groups) segregated with the TEL/AML1-positive SR group and not with the HR patient group. This is consistent with the fusion transcript affecting the gene expression profile (data not shown). Similarly, we found that patient 9, a TEL/AML1-negative patient, clustered within the TEL/AML1 branch and that patient 17, a TEL/AML1-postive patient, did not segregate into the TEL/AML1 branch. RT-PCR, using a different set of primers in a different laboratory, confirmed the presence of a TEL/AML1 transcript in patient 17 and its absence from patient 9; this indicates some heterogeneity in the TEL/AML1 group (data not shown). To avoid heterogeneity bias associated with particular patients and to highlight general processes, patients 9 and 17 were withdrawn from the two-class SAM gene-selection step comparing the TEL/AML1-positive group with the TEL/AML1-negative group. However, the data for these two patients were included in the final HC representation. To increase the robustness of gene-selection step, two cut-offs were applied successively, consistent with a 1.7-fold change, to exclude genes that varied little between the samples, (FC > 1.7), with or without a Q-value filter (Qvalue < 0.02) limiting the number of genes selected (Figure 1). This gave two TEL/AML1 gene sets, one of 181 genes and the other of 103 genes. These gene sets were used for hierarchical clustering representation of patient Set-A. Because the Set-A cohort was small, we validated our second selection (181 genes) by estimating the Benjamini and Hochberg false discovery rate (FDR): this value was consistently low (3.19% indicating only six false positives among the 181 genes designated as significant, data not shown). Both gene sets (181; 103) were able to cluster the TEL/AML1-positive Set-A patients, other than patients 9 and 17, in one branch. Hierarchical clustering highlighted 74 distinct genes among the 181 selected and they were separated into two clusters (data not shown). With the group of 103 selected genes, hierarchical clustering highlighted two clusters (44 distinct genes) able to group TEL/AML1-positive ALL (each cluster corresponds to a single branch of the hierarchical tree in which intercluster distance directly correlates with dissimilarity in gene expression) (Figure 2A). A resampling-based procedure (bootsrapping) was used to assess reproducibility (data not shown). Only these two restricted gene sets, of 74 and 44 genes, which correspond to a different profile of expression behavior associated with the presence of a TEL/AML1 chromosomal rearrangement, were able on their own to cluster the TEL/AML1 Set-A patients as previously and the TEL/AML1 Set-B patients into one branch. They were also able to segregate, with 100% reproducibility, the TEL/AML1 Set-A and -B patients together in the same branch, with the exceptions of patients 9 and 17 (Figure 2B).

Bottom Line: We compared the leukemia cell gene expression profiles of 16 TEL/AML1-positive ALL patients to those of 44 TEL/AML1-negative patients, whose blast cells did not contain any additional recurrent translocation.These results were first confirmed by the analysis of an additional microarray data-set (7 patient samples) and second by real-time RT-PCR quantification and clustering using an independent set (27 patient samples).Gene expression analyses of leukemia cells from 60 children with TEL/AML1-positive and -negative B-lineage ALL led to the identification of five biological processes, associated with 14 validated genes characterizing and highlighting the biology of the TEL/AML1-positive ALL sub-group.

View Article: PubMed Central - HTML - PubMed

Affiliation: CNRS UMR 6061 Laboratoire de Génétique et Développement, Equipe Régulation transcriptionnelle et oncogenèse, Université de Rennes-1, Faculté de Médecine, IFR140 GFAS, 2 av du Pr Léon Bernard, CS 34317, Rennes cedex, France. virginie.gandemer@chu-rennes.fr

ABSTRACT

Background: The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of ETV6 (TEL) and RUNX1 (AML1) genes and defines a relatively uniform category, although only some patients suffer very late relapse. TEL/AML1-positive patients are thus an interesting subgroup to study, and such studies should elucidate the biological processes underlying TEL/AML1 pathogenesis. We report an analysis of gene expression in 60 children with B-lineage ALL using Agilent whole genome oligo-chips (44K-G4112A) and/or real time RT-PCR.

Results: We compared the leukemia cell gene expression profiles of 16 TEL/AML1-positive ALL patients to those of 44 TEL/AML1-negative patients, whose blast cells did not contain any additional recurrent translocation. Microarray analyses of 26 samples allowed the identification of genes differentially expressed between the TEL/AML1-positive and negative ALL groups. Gene enrichment analysis defined five enriched GO categories: cell differentiation, cell proliferation, apoptosis, cell motility and response to wounding, associated with 14 genes -RUNX1, TCFL5, TNFRSF7, CBFA2T3, CD9, SCARB1, TP53INP1, ACVR1C, PIK3C3, EGFL7, SEMA6A, CTGF, LSP1, TFPI - highlighting the biology of the TEL/AML1 sub-group. These results were first confirmed by the analysis of an additional microarray data-set (7 patient samples) and second by real-time RT-PCR quantification and clustering using an independent set (27 patient samples). Over-expression of RUNX1 (AML1) was further investigated and in one third of the patients correlated with cytogenetic findings.

Conclusion: Gene expression analyses of leukemia cells from 60 children with TEL/AML1-positive and -negative B-lineage ALL led to the identification of five biological processes, associated with 14 validated genes characterizing and highlighting the biology of the TEL/AML1-positive ALL sub-group.

Show MeSH
Related in: MedlinePlus