Freitag, 14. August 2015

Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1

Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1



Introduction

Skeletal muscle cell differentiation is impaired by elevated levels of the inflammatory cytokine tumor necrosis factor-α (TNF-α) with pathological significance in chronic diseases or inherited muscle disorders. Insulin like growth factor-1 (IGF1) positively regulates muscle cell differentiation. Both, TNF-α and IGF1 affect gene and microRNA (miRNA) expression in this process. However, computational prediction of miRNA-mRNA relations is challenged by false positives and targets which might be irrelevant in the respective cellular transcriptome context. Thus, this study is focused on functional information about miRNA affected target transcripts by integrating miRNA and mRNA expression profiling data.

Methodology/Principal Findings

Murine skeletal myocytes PMI28 were differentiated for 24 hours with concomitant TNF-α or IGF1 treatment. Both, mRNA and miRNA expression profiling was performed. The data-driven integration of target prediction and paired mRNA/miRNA expression profiling data revealed that i) the quantity of predicted miRNA-mRNA relations was reduced, ii) miRNA targets with a function in cell cycle and axon guidance were enriched, iii) differential regulation of anti-differentiation miR-155-5p and miR-29b-3p as well as pro-differentiation miR-335-3p, miR-335-5p, miR-322-3p, and miR-322-5p seemed to be of primary importance during skeletal myoblast differentiation compared to the other miRNAs, iv) the abundance of targets and affected biological processes was miRNA specific, and v) subsets of miRNAs may collectively regulate gene expression.

Conclusions

Joint analysis of mRNA and miRNA profiling data increased the process-specificity and quality of predicted relations by statistically selecting miRNA-target interactions. Moreover, this study revealed miRNA-specific predominant biological implications in skeletal muscle cell differentiation and in response to TNF-α or IGF1 treatment. Furthermore, myoblast differentiation-associated miRNAs are suggested to collectively regulate gene clusters and targets associated with enriched specific gene ontology terms or pathways. Predicted miRNA functions of this study provide novel insights into defective regulation at the transcriptomic level during myocyte proliferation and differentiation due to inflammatory stimuli.

Donnerstag, 13. August 2015

Exosome and microRNA transfer from paracrine & endocrine to cross-kingdom communication


Exosome and microRNA transfer
from paracrine & endocrine to cross-kingdom communication

In multicellular organisms, the cell-to-cell communication is of particular importance for any physiological process, and the proper organization of the entire organism. Numerous studies over the past decade suggest a horizontal transfer of cellular secreted microRNAs between cells, tissues and organs. Hence extracellular RNAs (primarily small non-coding RNAs) represent a novel form of inter-cellular communication by transferring genetic information from a donor cell to a recipient cell. This points to an important new role for small RNAs in inter-cellular communication on the paracrine- and endocrine-level.

Para- and endocrine communication
Small RNAs (primary microRNAs, piRNAs and other small RNA families) can be exported out of the donor cells and transported by various carriers, e.g. membrane-derived vesicles (exosomes, microvesicles, ectosomes, apoptotic bodies, and more), microRNA-binding protein complexes (RBP), or high density lipoproteins (HDL). Secreted microRNAs can be delivered into recipient cells where they function as endogenous microRNAs, simultaneously regulating multiple target genes or signaling pathways.

Cross-kingdom communication
In prokaryotes, this molecular signaling is typically referred to as quorum sensing, whereas in eukaryotic cells, the molecular communication occurs through hormones and cytokines. Recently various publications report that microRNAs can also be transmitted from one species to another, inducing signal interference in distant species, even in a cross-kingdom manner. This new mode of cross-species communication might mediate symbiotic and pathogenic relationships between various organisms. 
This can be of enormous importance in the inter-species communication of microorganisms and their hosts or by diet-derived small RNAs. Higher organisms are constantly under attack from pathogens, resulting in severe consequences on global human or veterinary health. Hence small RNA mediated RNA interference (RNAi) is a conserved regulatory mechanism that is involved in almost all eukaryotic cellular processes, including host immunity and pathogen virulence. Recent evidence supports the significant contribution of small RNAs and RNAi to the communication between hosts and some eukaryotic pathogens or symbiotic microorganisms. Mobile silencing signals - most likely small RNAs - are capable of translocating from the host to its interacting organism, and vice versa.

Donnerstag, 6. August 2015

New Design -- qPCR & NGS eConferences series 2010 - 2015


We are presenting the qPCR & NGS eConferences series 2010 - 2015 via video stream!

eConferences.de

Amplify your knowledge in qPCR, dPCR and NGS!

This streaming portal is dedicated to scientists from the community of qPCR, digital PCR, Next Generation Sequencing (NGS), MicroGenomics (MG) and Molecular Diagnostics (MDx). You’ll find here all the records from around 280 presentations held at qPCR & NGS and MG Events in the past years – qPCR 2010 in Vienna, qPCR 2011, qPCR & NGS 2013 and qPCR & NGS 2015 in Freising-Weihenstephan, and MicroGenomics 2014 in Paris.

We provide the presentations via movie streaming technology in high quality – high resolution and perfect sound quality in high speed – on any internet browser or mobile device, including Android or iOS.






Mittwoch, 22. Juli 2015

Free available talks held at qPCR & NGS 2015 Event

qPCR & NGS 2015 Event
“Advanced Molecular Diagnostics for Biomarker Discovery”
7th international qPCR & NGS Event
Symposium & Industrial Exhibition & Application Workshops


Digital PCR
  http://www.econferences.de/digital-pcr-2015/
Optimisation, MIQE and Quality Control Strategies in qPCR
  http://www.econferences.de/optimisation-miqe-qc-strategies-in-qpcr-2015/
qPCR Biostatistics and BioInformatics
  http://www.econferences.de/qpcr-biostatistics-bioinformatics-2015/



Mittwoch, 15. Juli 2015

RNA Interference Off-target Screening using Principal Component Analysis | Open Access | OMICS Publishing Group

RNA Interference Off-target Screening using Principal Component Analysis
Jakob Müller* and Michael W. Pfaffl
Physiology Weihenstephan, Technische Universität München, Research Center for Nutrition and Food Science, Weihenstephaner Berg 3, 85350 Freising, Germany
Corresponding Author :Jakob Müller
Physiology Weihenstephan
Technische Universität München
Research Center for Nutrition and Food Science
Weihenstephaner Berg 3, 85350 Freising, Germany
 
Citation: Müller J, Pfaffl MW (2012) RNA Interference Off-target Screening using Principal Component Analysis. J Data Mining Genomics Proteomics 3:116. doi: 10.4172/2153-0602.1000116


RNA Interference Off-target Screening using Principal Component Analysis | Open Access | OMICS Publishing Group