Limits...
MicroRNA expression profiles of serum from patients before and after chemotherapy.

Diener Y, Walenda T, Jost E, Brümmendorf TH, Bosio A, Wagner W, Bissels U - Genom Data (2015)

Bottom Line: We wondered if microRNAs (miRNAs) circulating in serum could account for this effect.The miRNA microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series accession number GSE57570.Here, we provide a detailed protocol of the miRNA microarray and data analysis.

View Article: PubMed Central - PubMed

Affiliation: Miltenyi Biotec GmbH, Bergisch Gladbach, Germany.

ABSTRACT
Recovery of the blood and immune system after chemotherapy requires proliferation of hematopoietic stem and progenitor cells (HPSCs). It has been shown that systemically released factors in serum after chemotherapy stimulate HSPC expansion in vitro. We wondered if microRNAs (miRNAs) circulating in serum could account for this effect. Therefore, we compared the miRNA expression profiles of serum from patients with hematologic malignancies before and after chemotherapy. In addition to a general decrease in miRNA expression after chemotherapy, we found 23 miRNAs to be significantly differentially expressed in serum before versus after chemotherapy. The miRNA microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series accession number GSE57570. Here, we provide a detailed protocol of the miRNA microarray and data analysis.

No MeSH data available.


Related in: MedlinePlus

Higher number of detected microRNAs in patients' sera before chemotherapy. VENN diagram presenting numbers of detected miRNAs in serum from healthy donors (healthy), patients before (BC) and after chemotherapy (AC). Total gene intensities were filtered for miRNAs with median expression ≠ 0.1 over all donors. Exclusively in healthy donors detected miRNAs (8) were either detected with low signal intensities (< 10) or characterized as viral RNAs (HSV and KSHV).
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4664708&req=5

f0005: Higher number of detected microRNAs in patients' sera before chemotherapy. VENN diagram presenting numbers of detected miRNAs in serum from healthy donors (healthy), patients before (BC) and after chemotherapy (AC). Total gene intensities were filtered for miRNAs with median expression ≠ 0.1 over all donors. Exclusively in healthy donors detected miRNAs (8) were either detected with low signal intensities (< 10) or characterized as viral RNAs (HSV and KSHV).

Mentions: In order to obtain background subtracted and outlier rejected signal intensities, the scanned microarray images were analyzed and processed with the Agilent feature extraction software (v10.7.3.1) using default parameters (protocol miRNA_107_Sep09 and Grid: 031181_D_F_20111226). The resulting raw Total Gene Signal intensities (SI, gTotalGeneSignal column) were exported to Microsoft Excel and filtered for detected miRNAs (SI ≠ 0.1). Analysis of the detected miRNAs revealed a lower number of miRNAs in serum taken after chemotherapy compared to serum before chemotherapy (Fig. 1) as well as decreased miRNA signal intensities after chemotherapy (Fig. 2A). This global decrease in miRNA expression levels significantly correlated with leucocyte numbers in the patients' blood, which might indicate that the observed alterations are caused by leukopenia. As we were interested in miRNAs significantly differentially expressed in serum before versus after chemotherapy independently from the disturbance in blood cell counts, the data were normalized to the array median as follows: (1) a filter was set for miRNAs which were detected with an SI ≠ 0.1 in all patient samples before and after chemotherapy (= 18 samples), giving 66 miRNAs in total (including Agilent positive controls: dmr, hur). (2) For each sample, the median over these 66 miRNAs was calculated. (3) The value of each single miRNA was divided through the second highest median value. The highest median value was not used as it presumably resulted from an outlier. For statistical analysis and to determine differentially expressed miRNAs, median normalized signal intensities were log2 transformed and subjected to Student's paired t-test using Microsoft Excel 2010. We found 23 miRNAs to be significantly differentially expressed in serum before versus after chemotherapy (P ≤ 0.01, Fig. 2B). The three most significantly differentially expressed miRNAs were miRNA-320c (P = 0.0002), miRNA-1275 (P = 0.0005), and miRNA-3663-3p (P = 0.0006), among which miR-320c and miR-1275 were downregulated and miR-3663-3p was upregulated after chemotherapy.


MicroRNA expression profiles of serum from patients before and after chemotherapy.

Diener Y, Walenda T, Jost E, Brümmendorf TH, Bosio A, Wagner W, Bissels U - Genom Data (2015)

Higher number of detected microRNAs in patients' sera before chemotherapy. VENN diagram presenting numbers of detected miRNAs in serum from healthy donors (healthy), patients before (BC) and after chemotherapy (AC). Total gene intensities were filtered for miRNAs with median expression ≠ 0.1 over all donors. Exclusively in healthy donors detected miRNAs (8) were either detected with low signal intensities (< 10) or characterized as viral RNAs (HSV and KSHV).
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664708&req=5

f0005: Higher number of detected microRNAs in patients' sera before chemotherapy. VENN diagram presenting numbers of detected miRNAs in serum from healthy donors (healthy), patients before (BC) and after chemotherapy (AC). Total gene intensities were filtered for miRNAs with median expression ≠ 0.1 over all donors. Exclusively in healthy donors detected miRNAs (8) were either detected with low signal intensities (< 10) or characterized as viral RNAs (HSV and KSHV).
Mentions: In order to obtain background subtracted and outlier rejected signal intensities, the scanned microarray images were analyzed and processed with the Agilent feature extraction software (v10.7.3.1) using default parameters (protocol miRNA_107_Sep09 and Grid: 031181_D_F_20111226). The resulting raw Total Gene Signal intensities (SI, gTotalGeneSignal column) were exported to Microsoft Excel and filtered for detected miRNAs (SI ≠ 0.1). Analysis of the detected miRNAs revealed a lower number of miRNAs in serum taken after chemotherapy compared to serum before chemotherapy (Fig. 1) as well as decreased miRNA signal intensities after chemotherapy (Fig. 2A). This global decrease in miRNA expression levels significantly correlated with leucocyte numbers in the patients' blood, which might indicate that the observed alterations are caused by leukopenia. As we were interested in miRNAs significantly differentially expressed in serum before versus after chemotherapy independently from the disturbance in blood cell counts, the data were normalized to the array median as follows: (1) a filter was set for miRNAs which were detected with an SI ≠ 0.1 in all patient samples before and after chemotherapy (= 18 samples), giving 66 miRNAs in total (including Agilent positive controls: dmr, hur). (2) For each sample, the median over these 66 miRNAs was calculated. (3) The value of each single miRNA was divided through the second highest median value. The highest median value was not used as it presumably resulted from an outlier. For statistical analysis and to determine differentially expressed miRNAs, median normalized signal intensities were log2 transformed and subjected to Student's paired t-test using Microsoft Excel 2010. We found 23 miRNAs to be significantly differentially expressed in serum before versus after chemotherapy (P ≤ 0.01, Fig. 2B). The three most significantly differentially expressed miRNAs were miRNA-320c (P = 0.0002), miRNA-1275 (P = 0.0005), and miRNA-3663-3p (P = 0.0006), among which miR-320c and miR-1275 were downregulated and miR-3663-3p was upregulated after chemotherapy.

Bottom Line: We wondered if microRNAs (miRNAs) circulating in serum could account for this effect.The miRNA microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series accession number GSE57570.Here, we provide a detailed protocol of the miRNA microarray and data analysis.

View Article: PubMed Central - PubMed

Affiliation: Miltenyi Biotec GmbH, Bergisch Gladbach, Germany.

ABSTRACT
Recovery of the blood and immune system after chemotherapy requires proliferation of hematopoietic stem and progenitor cells (HPSCs). It has been shown that systemically released factors in serum after chemotherapy stimulate HSPC expansion in vitro. We wondered if microRNAs (miRNAs) circulating in serum could account for this effect. Therefore, we compared the miRNA expression profiles of serum from patients with hematologic malignancies before and after chemotherapy. In addition to a general decrease in miRNA expression after chemotherapy, we found 23 miRNAs to be significantly differentially expressed in serum before versus after chemotherapy. The miRNA microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series accession number GSE57570. Here, we provide a detailed protocol of the miRNA microarray and data analysis.

No MeSH data available.


Related in: MedlinePlus