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Comparison of a healthy miRNome with melanoma patient miRNomes: are microRNAs suitable serum biomarkers for cancer?

Margue C, Reinsbach S, Philippidou D, Beaume N, Walters C, Schneider JG, Nashan D, Behrmann I, Kreis S - Oncotarget (2015)

Bottom Line: We found characteristic signatures with excellent prognostic scores only in late stage but not in early stage melanoma patients.Upon comparison of melanoma tissue miRNomes with matching serum samples, several miRNAs were identified to be exclusively tissue-derived (miR-30b-5p, miR-374a-5p and others) while others had higher expression levels in serum (miR-3201 and miR-122-5p).Here we have compiled a healthy and widely applicable miRNome from serum samples and we provide strong evidence that levels of cell-free miRNAs only change significantly at later stages of melanoma progression, which has serious implications for miRNA biomarker studies in cancer.

View Article: PubMed Central - PubMed

Affiliation: Life Sciences Research Unit, University of Luxembourg, Luxembourg.

ABSTRACT
MiRNAs are increasingly recognized as biomarkers for the diagnosis of cancers where they are profiled from tumor tissue (intracellular miRNAs) or serum/plasma samples (extracellular miRNAs). To improve detection of reliable biomarkers from blood samples, we first compiled a healthy reference miRNome and established a well-controlled analysis pipeline allowing for standardized quantification of circulating miRNAs. Using whole miRNome and custom qPCR arrays, miRNA expression profiles were analyzed in 126 serum, whole blood and tissue samples of healthy volunteers and melanoma patients and in primary melanocyte and keratinocyte cell lines. We found characteristic signatures with excellent prognostic scores only in late stage but not in early stage melanoma patients. Upon comparison of melanoma tissue miRNomes with matching serum samples, several miRNAs were identified to be exclusively tissue-derived (miR-30b-5p, miR-374a-5p and others) while others had higher expression levels in serum (miR-3201 and miR-122-5p). Here we have compiled a healthy and widely applicable miRNome from serum samples and we provide strong evidence that levels of cell-free miRNAs only change significantly at later stages of melanoma progression, which has serious implications for miRNA biomarker studies in cancer.

No MeSH data available.


Related in: MedlinePlus

Overview of study designNumbers in brackets indicate number of separate samples included in pools. Individual melanoma patient serum samples analysed on custom qPCR arrays comprise 4 stage 0, 11 stage I, 17 stage II, 11 stage III and 9 stage IV samples.
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Figure 1: Overview of study designNumbers in brackets indicate number of separate samples included in pools. Individual melanoma patient serum samples analysed on custom qPCR arrays comprise 4 stage 0, 11 stage I, 17 stage II, 11 stage III and 9 stage IV samples.

Mentions: Fig. 1 summarises the study design, the number and types of samples analysed by whole miRNome qPCR arrays and by customized qPCR arrays representing 88 miRNAs, selected to serve as potential biomarkers for the diagnosis of melanoma. Here, extensive quality control steps for sample collection, processing, data acquisition and analysis were applied in order to obtain robust and reproducible results, indicating whether secreted miRNAs could indeed be suitable biomarkers for melanoma. We chose a qPCR array platform with pre-amplification of mature miRNAs suitable for quantification of the typically low miRNA amounts in cell-free samples. Previous in-house data with hybridization microarrays and RNA-Seq revealed that qPCR would be the most useful technique for this purpose. In accordance, a recent comprehensive comparison of 12 commercially available miRNA profiling platforms also showed qPCR arrays to perform well in terms of reproducibly, sensitively and specifically quantifying low copy number miRNAs [26].


Comparison of a healthy miRNome with melanoma patient miRNomes: are microRNAs suitable serum biomarkers for cancer?

Margue C, Reinsbach S, Philippidou D, Beaume N, Walters C, Schneider JG, Nashan D, Behrmann I, Kreis S - Oncotarget (2015)

Overview of study designNumbers in brackets indicate number of separate samples included in pools. Individual melanoma patient serum samples analysed on custom qPCR arrays comprise 4 stage 0, 11 stage I, 17 stage II, 11 stage III and 9 stage IV samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494926&req=5

Figure 1: Overview of study designNumbers in brackets indicate number of separate samples included in pools. Individual melanoma patient serum samples analysed on custom qPCR arrays comprise 4 stage 0, 11 stage I, 17 stage II, 11 stage III and 9 stage IV samples.
Mentions: Fig. 1 summarises the study design, the number and types of samples analysed by whole miRNome qPCR arrays and by customized qPCR arrays representing 88 miRNAs, selected to serve as potential biomarkers for the diagnosis of melanoma. Here, extensive quality control steps for sample collection, processing, data acquisition and analysis were applied in order to obtain robust and reproducible results, indicating whether secreted miRNAs could indeed be suitable biomarkers for melanoma. We chose a qPCR array platform with pre-amplification of mature miRNAs suitable for quantification of the typically low miRNA amounts in cell-free samples. Previous in-house data with hybridization microarrays and RNA-Seq revealed that qPCR would be the most useful technique for this purpose. In accordance, a recent comprehensive comparison of 12 commercially available miRNA profiling platforms also showed qPCR arrays to perform well in terms of reproducibly, sensitively and specifically quantifying low copy number miRNAs [26].

Bottom Line: We found characteristic signatures with excellent prognostic scores only in late stage but not in early stage melanoma patients.Upon comparison of melanoma tissue miRNomes with matching serum samples, several miRNAs were identified to be exclusively tissue-derived (miR-30b-5p, miR-374a-5p and others) while others had higher expression levels in serum (miR-3201 and miR-122-5p).Here we have compiled a healthy and widely applicable miRNome from serum samples and we provide strong evidence that levels of cell-free miRNAs only change significantly at later stages of melanoma progression, which has serious implications for miRNA biomarker studies in cancer.

View Article: PubMed Central - PubMed

Affiliation: Life Sciences Research Unit, University of Luxembourg, Luxembourg.

ABSTRACT
MiRNAs are increasingly recognized as biomarkers for the diagnosis of cancers where they are profiled from tumor tissue (intracellular miRNAs) or serum/plasma samples (extracellular miRNAs). To improve detection of reliable biomarkers from blood samples, we first compiled a healthy reference miRNome and established a well-controlled analysis pipeline allowing for standardized quantification of circulating miRNAs. Using whole miRNome and custom qPCR arrays, miRNA expression profiles were analyzed in 126 serum, whole blood and tissue samples of healthy volunteers and melanoma patients and in primary melanocyte and keratinocyte cell lines. We found characteristic signatures with excellent prognostic scores only in late stage but not in early stage melanoma patients. Upon comparison of melanoma tissue miRNomes with matching serum samples, several miRNAs were identified to be exclusively tissue-derived (miR-30b-5p, miR-374a-5p and others) while others had higher expression levels in serum (miR-3201 and miR-122-5p). Here we have compiled a healthy and widely applicable miRNome from serum samples and we provide strong evidence that levels of cell-free miRNAs only change significantly at later stages of melanoma progression, which has serious implications for miRNA biomarker studies in cancer.

No MeSH data available.


Related in: MedlinePlus