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Impact of cellular miRNAs on circulating miRNA biomarker signatures.

Duttagupta R, Jiang R, Gollub J, Getts RC, Jones KW - PLoS ONE (2011)

Bottom Line: Correlations between tumor-associated genomic/epigenetic/transcriptional changes and alterations in CNA levels are strong predictors of the utility of this biomarker class as promising clinical indicators.We find that measurement of circulating miRNA levels are frequently confounded by varying levels of cellular miRNAs of different hematopoietic origins.Cellular miRNA signatures in cohorts of normal individuals are catalogued and the abundance and gender specific expression of bona fide circulating markers explored after calibrating the signal for this interfering class.

View Article: PubMed Central - PubMed

Affiliation: Applied Research, Affymetrix Inc, Santa Clara, California, United States of America.

ABSTRACT
Effective diagnosis and surveillance of complex multi-factorial disorders such as cancer can be improved by screening of easily accessible biomarkers. Highly stable cell free Circulating Nucleic Acids (CNA) present as both RNA and DNA species have been discovered in the blood and plasma of humans. Correlations between tumor-associated genomic/epigenetic/transcriptional changes and alterations in CNA levels are strong predictors of the utility of this biomarker class as promising clinical indicators. Towards this goal microRNAs (miRNAs) representing a class of naturally occurring small non-coding RNAs of 19-25 nt in length have emerged as an important set of markers that can associate their specific expression profiles with cancer development. In this study we investigate some of the pre-analytic considerations for isolating plasma fractions for the study of miRNA biomarkers. We find that measurement of circulating miRNA levels are frequently confounded by varying levels of cellular miRNAs of different hematopoietic origins. In order to assess the relative proportions of this cell-derived class, we have fractionated whole blood into plasma and its ensuing sub-fractions. Cellular miRNA signatures in cohorts of normal individuals are catalogued and the abundance and gender specific expression of bona fide circulating markers explored after calibrating the signal for this interfering class. A map of differentially expressed profiles is presented and the intrinsic variability of circulating miRNA species investigated in subsets of healthy males and females.

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Concordance of expression levels of circulating miRNA species between the CS, S1 and P1 fractions.(A–D) Heat map of Spearman's Rank Correlation coefficients for the highest expressing 20, 35, 50 and 100 miRNAs present in CS, P1 and S1 fractions after removal of contaminant features. The correlation values are shown in the bar scale.
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pone-0020769-g003: Concordance of expression levels of circulating miRNA species between the CS, S1 and P1 fractions.(A–D) Heat map of Spearman's Rank Correlation coefficients for the highest expressing 20, 35, 50 and 100 miRNAs present in CS, P1 and S1 fractions after removal of contaminant features. The correlation values are shown in the bar scale.

Mentions: In order to ensure that sub-fractionation of the CS into the S1 and P1 categories did not result in the loss of true circulating miRNA species, we assessed the concordance in intensities between the CS and ensuing S1 and P1 fractions to determine their extent of similarity. Spearman's Rank Correlation analysis was performed on all detected miRNAs after removal of contaminant features in the 3 samples (CS, S1 and P1). The filtered miRNAs were first stratified into different intensity bins consisting of highest expressing 20, 35, 50 and 100 miRNAs based on average intensity levels across all fractions (Fig. 3A–D) and correlation values calculated for each pair. We observe strong and improved rank order correlations between the CS and S1 fractions (rank correlations >0.6) compared to the CS, S1 and P1 fraction pairs (rank correlations <0.0). This implies that the composition of the P1 fraction is distinct from the CS and S1 fractions and consists of unique species of miRNAs. In contrast the strong rank-order correlation between the CS and the S1 class demonstrates the presence of homogenous populations of miRNAs, indicating a preservation of miRNA species between the two plasma fractions through the fractionation process.


Impact of cellular miRNAs on circulating miRNA biomarker signatures.

Duttagupta R, Jiang R, Gollub J, Getts RC, Jones KW - PLoS ONE (2011)

Concordance of expression levels of circulating miRNA species between the CS, S1 and P1 fractions.(A–D) Heat map of Spearman's Rank Correlation coefficients for the highest expressing 20, 35, 50 and 100 miRNAs present in CS, P1 and S1 fractions after removal of contaminant features. The correlation values are shown in the bar scale.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3117799&req=5

pone-0020769-g003: Concordance of expression levels of circulating miRNA species between the CS, S1 and P1 fractions.(A–D) Heat map of Spearman's Rank Correlation coefficients for the highest expressing 20, 35, 50 and 100 miRNAs present in CS, P1 and S1 fractions after removal of contaminant features. The correlation values are shown in the bar scale.
Mentions: In order to ensure that sub-fractionation of the CS into the S1 and P1 categories did not result in the loss of true circulating miRNA species, we assessed the concordance in intensities between the CS and ensuing S1 and P1 fractions to determine their extent of similarity. Spearman's Rank Correlation analysis was performed on all detected miRNAs after removal of contaminant features in the 3 samples (CS, S1 and P1). The filtered miRNAs were first stratified into different intensity bins consisting of highest expressing 20, 35, 50 and 100 miRNAs based on average intensity levels across all fractions (Fig. 3A–D) and correlation values calculated for each pair. We observe strong and improved rank order correlations between the CS and S1 fractions (rank correlations >0.6) compared to the CS, S1 and P1 fraction pairs (rank correlations <0.0). This implies that the composition of the P1 fraction is distinct from the CS and S1 fractions and consists of unique species of miRNAs. In contrast the strong rank-order correlation between the CS and the S1 class demonstrates the presence of homogenous populations of miRNAs, indicating a preservation of miRNA species between the two plasma fractions through the fractionation process.

Bottom Line: Correlations between tumor-associated genomic/epigenetic/transcriptional changes and alterations in CNA levels are strong predictors of the utility of this biomarker class as promising clinical indicators.We find that measurement of circulating miRNA levels are frequently confounded by varying levels of cellular miRNAs of different hematopoietic origins.Cellular miRNA signatures in cohorts of normal individuals are catalogued and the abundance and gender specific expression of bona fide circulating markers explored after calibrating the signal for this interfering class.

View Article: PubMed Central - PubMed

Affiliation: Applied Research, Affymetrix Inc, Santa Clara, California, United States of America.

ABSTRACT
Effective diagnosis and surveillance of complex multi-factorial disorders such as cancer can be improved by screening of easily accessible biomarkers. Highly stable cell free Circulating Nucleic Acids (CNA) present as both RNA and DNA species have been discovered in the blood and plasma of humans. Correlations between tumor-associated genomic/epigenetic/transcriptional changes and alterations in CNA levels are strong predictors of the utility of this biomarker class as promising clinical indicators. Towards this goal microRNAs (miRNAs) representing a class of naturally occurring small non-coding RNAs of 19-25 nt in length have emerged as an important set of markers that can associate their specific expression profiles with cancer development. In this study we investigate some of the pre-analytic considerations for isolating plasma fractions for the study of miRNA biomarkers. We find that measurement of circulating miRNA levels are frequently confounded by varying levels of cellular miRNAs of different hematopoietic origins. In order to assess the relative proportions of this cell-derived class, we have fractionated whole blood into plasma and its ensuing sub-fractions. Cellular miRNA signatures in cohorts of normal individuals are catalogued and the abundance and gender specific expression of bona fide circulating markers explored after calibrating the signal for this interfering class. A map of differentially expressed profiles is presented and the intrinsic variability of circulating miRNA species investigated in subsets of healthy males and females.

Show MeSH
Related in: MedlinePlus