Multiparametric diagnostics of cardiomyopathies by microRNA signatures

Siegismund, Christine S.; Rohde, Maria; Kühl, Uwe; Laßner, Dirk

doi:10.1007/s00604-014-1249-y

Cited by 4 publications

(9 citation statements)

References 32 publications

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“…The first qPCR assay to quantify miRNAs was developed almost a decade ago [51], and subsequent protocols for using relative and absolute quantification have been developed [52]. miRNAs have been successfully identified as possible biomarkers for cancer [53], autologous transfusion [54], diabetes [51] and cardiomyopathies [55]. In addition to miRNAs, a large number of different non-coding RNAs have been described, where many show regulatory functions.…”

Section: Applications Of Qpcrmentioning

confidence: 99%

A survey of tools for the analysis of quantitative PCR (qPCR) data

Pabinger

Rödiger

Kriegner

et al. 2014

Biomolecular Detection and Quantification

155

119

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Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions.Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR.Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

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Section: Applications Of Qpcrmentioning

confidence: 99%

A survey of tools for the analysis of quantitative PCR (qPCR) data

Pabinger

Rödiger

Kriegner

et al. 2014

Biomolecular Detection and Quantification

155

119

View full text Add to dashboard Cite

show abstract

“…Disease-specific miRNA signatures in tissues differ significantly from those in blood cells, serum or other body fluids of the same patient and therefore have their own specificity for the present condition [26] [74]. As shown for Takotsubo cardiomyopathy, a potentially life-threatening disease, which is clinically indistinguishable from acute myocardial infarction, circulating miRNAs are found which allow a differentiation of Takotsubo cardiomyopathy and myocardial infarction [83].…”

Section: Biomarker Based Diagnostics For Personalized Medicinementioning

confidence: 99%

“…Multiparametric diagnostic systems, measuring differentially expressed genes or miRNAs, may thus become a valuable diagnostic tool of the future due to its high predictive value in respect to clinical course, treatment decisions and therapy monitoring [74].…”

Section: Biomarker Based Diagnostics For Personalized Medicinementioning

confidence: 99%

See 1 more Smart Citation

Myocarditis—Personalized Medicine by Expanded Endomyocardial Biopsy Diagnostics

Laßner¹,

Rohde²,

Siegismund³

et al. 2014

WJCD

Self Cite

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Myocarditis and dilated cardiomyopathy (DCM) are acute or chronic disorders of myocardium. The gold standard for final confirmation of causative reasons of these heart muscle diseases is the endomyocardial biopsy (EMB) analysis. Due to focal pathology, diagnostics are failing if the EMB does not contain the area of interest. Personalized medicine comprises the genetic information together with the phenotypic and environmental factors to yield a tailored healthcare for each individual and removes the limitations of the "one-size-fits-all" therapy approach. This provides the opportunity to translate therapies from bench to bedside, to diagnose and predict disease, and to improve patient-tailored treatments based on the unique signatures of a patient's disease. Furthermore, novel treatment schedules can be identified which have eventually the chance to enhance long-term survivals. Global biomarkers such as specific gene expression signatures or miRNA profiles not only have the potential to reduce this problem but also add valuable information for individualized therapy decisions. In future, multiplex approaches allowing rapid and absolutely reliable identification of inflammatory or virally-induced myocardial diseases will replace singleplex methods such as direct detection of viral genomes in one single biopsy. Gene or miRNA profiles are upcoming diagnostic biomarkers for cardiomyopathies which are not only detectable in tissue samples but in body fluids as well. Consequently, a systemic diagnostic approach by determination of distinct expression pattern in e.g., peripheral blood samples will support the characterization of distinct cardiomyopathies by means of non-invasive methods.

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“…miRNA profiling can serve as a new exciting tool in modern diagnostics, which is comparable to gene expression analysis but with less amount of analytes. In addition, approximately 2500 human mature miRNAs have been discovered so far, which seems to be relatively small in number compared to the enormous number of genes discovered [15] , [16] , [17] , [18] , [19] , [20] , [21] .…”

Section: Introductionmentioning

confidence: 99%

Absent MicroRNAs in Different Tissues of Patients with Acquired Cardiomyopathy

Siegismund

Rohde

Kühl

et al. 2016

Genomics, Proteomics &Amp; Bioinformatics

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MicroRNAs (miRNAs) can be found in a wide range of tissues and body fluids, and their specific signatures can be used to determine diseases or predict clinical courses. The miRNA profiles in biological samples (tissue, serum, peripheral blood mononuclear cells or other body fluids) differ significantly even in the same patient and therefore have their own specificity for the presented condition. Complex profiles of deregulated miRNAs are of high interest, whereas the importance of non-expressed miRNAs was ignored. Since miRNAs regulate gene expression rather negatively, absent miRNAs could indicate genes with unaltered expression that therefore are normally expressed in specific compartments or under specific disease situations. For the first time, non-detectable miRNAs in different tissues and body fluids from patients with different diseases (cardiomyopathies, Alzheimer’s disease, bladder cancer, and ocular cancer) were analyzed and compared in this study. miRNA expression data were generated by microarray or TaqMan PCR-based platforms. Lists of absent miRNAs of primarily cardiac patients (myocardium, blood cells, and serum) were clustered and analyzed for potentially involved pathways using two prediction platforms, i.e., miRNA enrichment analysis and annotation tool (miEAA) and DIANA miRPath. Extensive search in biomedical publication databases for the relevance of non-expressed miRNAs in predicted pathways revealed no evidence for their involvement in heart-related pathways as indicated by software tools, confirming proposed approach.

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Multiparametric diagnostics of cardiomyopathies by microRNA signatures

Cited by 4 publications

References 32 publications

A survey of tools for the analysis of quantitative PCR (qPCR) data

A survey of tools for the analysis of quantitative PCR (qPCR) data

Myocarditis—Personalized Medicine by Expanded Endomyocardial Biopsy Diagnostics

Absent MicroRNAs in Different Tissues of Patients with Acquired Cardiomyopathy

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