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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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Related in: MedlinePlus

Validation of gene expression data of stromal cells by real-time RT-PCR. Comparison of gene expression obtained from real-time RT-PCR (black bars) and microarray experiments (gray bars) for four select genes (names indicated at bottom) in stromal cells of MDS-RARS patients and of healthy individuals. The positive and negative fold change values indicate up- or down-regulation of expression in MDS-RARS patients in relation to the expression in healthy individuals, respectively.
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Figure 6: Validation of gene expression data of stromal cells by real-time RT-PCR. Comparison of gene expression obtained from real-time RT-PCR (black bars) and microarray experiments (gray bars) for four select genes (names indicated at bottom) in stromal cells of MDS-RARS patients and of healthy individuals. The positive and negative fold change values indicate up- or down-regulation of expression in MDS-RARS patients in relation to the expression in healthy individuals, respectively.

Mentions: Four transcripts were chosen to validate microarray data by real-time RT-PCR. RNA extracted from stromal cells from 5 MDS-RARS patients (nos. 3-7; Table 1) was used for validation studies; all transcripts were confirmed by real-time RT-PCR (Figure 6).


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)

Validation of gene expression data of stromal cells by real-time RT-PCR. Comparison of gene expression obtained from real-time RT-PCR (black bars) and microarray experiments (gray bars) for four select genes (names indicated at bottom) in stromal cells of MDS-RARS patients and of healthy individuals. The positive and negative fold change values indicate up- or down-regulation of expression in MDS-RARS patients in relation to the expression in healthy individuals, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Validation of gene expression data of stromal cells by real-time RT-PCR. Comparison of gene expression obtained from real-time RT-PCR (black bars) and microarray experiments (gray bars) for four select genes (names indicated at bottom) in stromal cells of MDS-RARS patients and of healthy individuals. The positive and negative fold change values indicate up- or down-regulation of expression in MDS-RARS patients in relation to the expression in healthy individuals, respectively.
Mentions: Four transcripts were chosen to validate microarray data by real-time RT-PCR. RNA extracted from stromal cells from 5 MDS-RARS patients (nos. 3-7; Table 1) was used for validation studies; all transcripts were confirmed by real-time RT-PCR (Figure 6).

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