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Identification of protein-coding and non-coding RNA expression profiles in CD34+ and in stromal cells in refractory anemia with ringed sideroblasts.

Baratti MO, Moreira YB, Traina F, Costa FF, Verjovski-Almeida S, Olalla-Saad ST - BMC Med Genomics (2010)

Bottom Line: Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia.In CD34+ cells of MDS-RARS patients, 216 genes were significantly differentially expressed (q-value <or= 0.01) in comparison to healthy individuals, of which 65 (30%) were non-coding transcripts.In stromal cells of MDS-RARS, 12 genes were significantly differentially expressed (q-value <or= 0.05) in comparison to healthy individuals, of which 3 (25%) were non-coding transcripts.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Internal Medicine, School of Medical Science, Hematology and Hemotherapy Center, University of Campinas, 13083-970 Campinas, SP, Brazil.

ABSTRACT

Background: Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia. Microarray technology has permitted a refined high-throughput mapping of the transcriptional activity in the human genome. Non-coding RNAs (ncRNAs) transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression, and in the regulation of exon-skipping and intron retention. Characterization of ncRNAs in progenitor cells and stromal cells of MDS patients could be strategic for understanding gene expression regulation in this disease.

Methods: In this study, gene expression profiles of CD34+ cells of 4 patients with MDS of refractory anemia with ringed sideroblasts (RARS) subgroup and stromal cells of 3 patients with MDS-RARS were compared with healthy individuals using 44 k combined intron-exon oligoarrays, which included probes for exons of protein-coding genes, and for non-coding RNAs transcribed from intronic regions in either the sense or antisense strands. Real-time RT-PCR was performed to confirm the expression levels of selected transcripts.

Results: In CD34+ cells of MDS-RARS patients, 216 genes were significantly differentially expressed (q-value

Conclusions: These results demonstrated, for the first time, the differential ncRNA expression profile between MDS-RARS and healthy individuals, in CD34+ cells and stromal cells, suggesting that ncRNAs may play an important role during the development of myelodysplastic syndromes.

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Differentially expressed transcripts in stromal cells of MDS-RARS patients and healthy individuals. The panel shows the expression matrix of 12 significantly differentially expressed genes in stromal cells of MDS-RARS patients compared to healthy individuals (SAM FDR <5% and fold change ≥1.7). Each row represents a single gene (9 protein-coding genes with names in black, and 3 ncRNAs in blue) and each column represents a separate stromal donor sample. Donor samples were clustered according to the correlation of expression profiles using the Unweighted Pair-Group Method, which resulted in two homogenous groups: MDS-RARS patients (3 columns at right) and healthy individuals (4 columns at left). Expression level of each gene is represented by the number of standard deviations above (red) or below (green) the average value for that gene across all samples. In MD-RARS patients, a total of 10 genes were up-regulated and 2 down-regulated.
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Figure 4: Differentially expressed transcripts in stromal cells of MDS-RARS patients and healthy individuals. The panel shows the expression matrix of 12 significantly differentially expressed genes in stromal cells of MDS-RARS patients compared to healthy individuals (SAM FDR <5% and fold change ≥1.7). Each row represents a single gene (9 protein-coding genes with names in black, and 3 ncRNAs in blue) and each column represents a separate stromal donor sample. Donor samples were clustered according to the correlation of expression profiles using the Unweighted Pair-Group Method, which resulted in two homogenous groups: MDS-RARS patients (3 columns at right) and healthy individuals (4 columns at left). Expression level of each gene is represented by the number of standard deviations above (red) or below (green) the average value for that gene across all samples. In MD-RARS patients, a total of 10 genes were up-regulated and 2 down-regulated.

Mentions: Stromal cells obtained from three MDS-RARS patients (nos. 4-6; Table 1) were compared with stromal cells of healthy individuals using the same custom-designed combined intron-exon expression oligoarrays and significance analysis. SAM combined with patient leave-one-out cross validation identified 12 significantly (q-value ≤ 0.05) differentially expressed genes (10 up-regulated and 2 down-regulated in stromal cells of MDS-RARS patients) (Figure 4; Additional file 3), of which 3 were ncRNAs (up-regulated in MDS-RARS patients) (Table 5). The low number of differentially expressed genes was mostly due to the high homogeneity of stromal cells from patients and donors (correlation coefficient between all donor and patient stromal samples = 0.93, contrasted to 0.9 of CD34+ cells, p = 10-5). The signature expression profile of protein-coding transcripts in MDS-RARS stromal cells revealed genes related to several biological processes, such as cell motility, DNA replication, protein amino acid phosphorylation and protein transport (Table 4).


Identification of protein-coding and non-coding RNA expression profiles in CD34+ and in stromal cells in refractory anemia with ringed sideroblasts.

Baratti MO, Moreira YB, Traina F, Costa FF, Verjovski-Almeida S, Olalla-Saad ST - BMC Med Genomics (2010)

Differentially expressed transcripts in stromal cells of MDS-RARS patients and healthy individuals. The panel shows the expression matrix of 12 significantly differentially expressed genes in stromal cells of MDS-RARS patients compared to healthy individuals (SAM FDR <5% and fold change ≥1.7). Each row represents a single gene (9 protein-coding genes with names in black, and 3 ncRNAs in blue) and each column represents a separate stromal donor sample. Donor samples were clustered according to the correlation of expression profiles using the Unweighted Pair-Group Method, which resulted in two homogenous groups: MDS-RARS patients (3 columns at right) and healthy individuals (4 columns at left). Expression level of each gene is represented by the number of standard deviations above (red) or below (green) the average value for that gene across all samples. In MD-RARS patients, a total of 10 genes were up-regulated and 2 down-regulated.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC2914047&req=5

Figure 4: Differentially expressed transcripts in stromal cells of MDS-RARS patients and healthy individuals. The panel shows the expression matrix of 12 significantly differentially expressed genes in stromal cells of MDS-RARS patients compared to healthy individuals (SAM FDR <5% and fold change ≥1.7). Each row represents a single gene (9 protein-coding genes with names in black, and 3 ncRNAs in blue) and each column represents a separate stromal donor sample. Donor samples were clustered according to the correlation of expression profiles using the Unweighted Pair-Group Method, which resulted in two homogenous groups: MDS-RARS patients (3 columns at right) and healthy individuals (4 columns at left). Expression level of each gene is represented by the number of standard deviations above (red) or below (green) the average value for that gene across all samples. In MD-RARS patients, a total of 10 genes were up-regulated and 2 down-regulated.
Mentions: Stromal cells obtained from three MDS-RARS patients (nos. 4-6; Table 1) were compared with stromal cells of healthy individuals using the same custom-designed combined intron-exon expression oligoarrays and significance analysis. SAM combined with patient leave-one-out cross validation identified 12 significantly (q-value ≤ 0.05) differentially expressed genes (10 up-regulated and 2 down-regulated in stromal cells of MDS-RARS patients) (Figure 4; Additional file 3), of which 3 were ncRNAs (up-regulated in MDS-RARS patients) (Table 5). The low number of differentially expressed genes was mostly due to the high homogeneity of stromal cells from patients and donors (correlation coefficient between all donor and patient stromal samples = 0.93, contrasted to 0.9 of CD34+ cells, p = 10-5). The signature expression profile of protein-coding transcripts in MDS-RARS stromal cells revealed genes related to several biological processes, such as cell motility, DNA replication, protein amino acid phosphorylation and protein transport (Table 4).

Bottom Line: Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia.In CD34+ cells of MDS-RARS patients, 216 genes were significantly differentially expressed (q-value <or= 0.01) in comparison to healthy individuals, of which 65 (30%) were non-coding transcripts.In stromal cells of MDS-RARS, 12 genes were significantly differentially expressed (q-value <or= 0.05) in comparison to healthy individuals, of which 3 (25%) were non-coding transcripts.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Internal Medicine, School of Medical Science, Hematology and Hemotherapy Center, University of Campinas, 13083-970 Campinas, SP, Brazil.

ABSTRACT

Background: Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia. Microarray technology has permitted a refined high-throughput mapping of the transcriptional activity in the human genome. Non-coding RNAs (ncRNAs) transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression, and in the regulation of exon-skipping and intron retention. Characterization of ncRNAs in progenitor cells and stromal cells of MDS patients could be strategic for understanding gene expression regulation in this disease.

Methods: In this study, gene expression profiles of CD34+ cells of 4 patients with MDS of refractory anemia with ringed sideroblasts (RARS) subgroup and stromal cells of 3 patients with MDS-RARS were compared with healthy individuals using 44 k combined intron-exon oligoarrays, which included probes for exons of protein-coding genes, and for non-coding RNAs transcribed from intronic regions in either the sense or antisense strands. Real-time RT-PCR was performed to confirm the expression levels of selected transcripts.

Results: In CD34+ cells of MDS-RARS patients, 216 genes were significantly differentially expressed (q-value

Conclusions: These results demonstrated, for the first time, the differential ncRNA expression profile between MDS-RARS and healthy individuals, in CD34+ cells and stromal cells, suggesting that ncRNAs may play an important role during the development of myelodysplastic syndromes.

Show MeSH
Related in: MedlinePlus