miR-181c Regulates the Mitochondrial Genome,Bioenergetics, and Propensity for Heart Failure In Vivo

MicroRNAs (miRNAs) are small non-coding RNAs, which inhibit the stability and/or translation of a mRNA. miRNAs have been found to play a powerful role in various cardiovascular diseases. Recently, we have demonstrated that a microRNA (miR-181c) can be encoded in the nucleus, processed to the mature form in the cytosol, translocated into the mitochondria, and ultimately can regulate mitochondrial gene expression. However the in vivo impact of miR-181c is unknown. Here we report an in-vivo method for administration of miR-181c in rats, which leads to reduced exercise capacity and signs of heart failure, by targeting the 3′-end of mt-COX1 (cytochrome c oxidase subunit 1). We cloned miR-181c and packaged it in lipid-based nanoparticles for systemic delivery. The plasmid DNA complexed nanovector shows no apparent toxicity. We find that the mRNA levels of mitochondrial complex IV genes in the heart, but not any other mitochondrial genes, are significantly altered with miR-181c overexpression, suggesting selective mitochondrial complex IV remodeling due to miR-181c targeting mt-COX1. Isolated heart mitochondrial studies showed significantly altered O₂-consumption, ROS production, matrix calcium, and mitochondrial membrane potential in miR-181c-treated animals. For the first time, this study shows that miRNA delivered to the heart in-vivo can lead to cardiac dysfunction by regulating mitochondrial genes.     

Pigment stratigraphy and trophic status: An evaluation of radionuclide‐dated lacustrine sediment

Sediment cores from the profundal region of relatively young (ca. 45 years), warm‐monomictic Lake Vechten were dated with Cs and ²¹⁰Pb and analyzed for major carotenoids, chlorophyll, and pheophytin. Vertical sediment accretion rates determined from a clay/sand horizon and from the radionuclide datings varied between 0.60 and 0.74 cm/year. Sedimentation rates based on paniculate matter collected in sediment traps agreed with results of the ¹³⁷Cs method with average values of respectively 2.9 and 2.3 kg dry weight m^‐2 year^‐1. It was concluded that the profundal sediment is fairly undisturbed. Pigments showed a severalfold increase from the deepest to the superficial sediment layers. Their profiles were compared with limnological data obtained during previous studies of Lake Vechten. Evidence was provided that the distribution of pigments reflected grossly the trophic history of the lake, which became more eutrophic during the last two decades. Pigment analyses of sediment cores may be a useful tool to rapidly obtain rough basic information on the recent trophic development of stratified lakes liable to eutrophication.     

Cysteine 203 of cyclophilin D is critical for cyclophilin D activation of the mitochondrial permeability transition pore

The mitochondrial permeability transition pore (mPTP) opening plays a critical role in mediating cell death during ischemia/reperfusion (I/R) injury. Our previous studies have shown that cysteine 203 of cyclophilin D (CypD), a critical mPTP mediator, undergoes protein S-nitrosylation (SNO). To investigate the role of cysteine 203 in mPTP activation, we mutated cysteine 203 of CypD to a serine residue (C203S) and determined its effect on mPTP opening. Treatment of WT mouse embryonic fibroblasts (MEFs) with H(2)O(2) resulted in an 50% loss of the mitochondrial calcein fluorescence, suggesting substantial activation of the mPTP. Consistent with the reported role of CypD in mPTP activation, CypD null (CypD(-/-)) MEFs exhibited significantly less mPTP opening. Addition of a nitric oxide donor, GSNO, to WT but not CypD(-/-) MEFs prior to H(2)O(2) attenuated mPTP opening. To test whether Cys-203 is required for this protection, we infected CypD(-/-) MEFs with a C203S-CypD vector. Surprisingly, C203S-CypD reconstituted MEFs were resistant to mPTP opening in the presence or absence of GSNO, suggesting a crucial role for Cys-203 in mPTP activation. To determine whether mutation of C203S-CypD would alter mPTP in vivo, we injected a recombinant adenovirus encoding C203S-CypD or WT CypD into CypD(-/-) mice via tail vein. Mitochondria isolated from livers of CypD(-/-) mice or mice expressing C203S-CypD were resistant to Ca(2+)-induced swelling as compared with WT CypD-reconstituted mice. Our results indicate that the Cys-203 residue of CypD is necessary for redox stress-induced activation of mPTP.     

MicroRNAs in cancer drug resistance: Basic evidence and clinical applications

Development of drug resistance has considerably limited the efficacy of cancer treatments, including chemotherapy and targeted therapies. Hence, understanding the molecular mechanisms underpinning the innate or the acquired resistance to these therapies is critical to improve drug efficiency and clinical outcomes. Several studies have implicated microRNAs (miRNA) in this process. MiRNAs repress gene expression by specific binding to complementary sequences in the 3' region of target messenger RNAs (mRNAs), followed by target mRNA degradation or blocked translation. By targeting molecules specific to a particular pathway within tumor cells, the new generation of cancer treatment strategies has shown significant advantages over conventional chemotherapy. However, the long-term efficacy of targeted therapies often remains poor, because tumor cells develop resistance to such therapeutics. Targeted therapies often involve monoclonal antibodies (mAbs), such as those blocking the ErB/HER tyrosine kinases, epidermal growth factor receptor (cetuximab) and HER2 (trastuzumab), and those inhibiting vascular endothelial growth factor receptor signaling (e.g., bevacizumab). Even though these are among the most used agents in tumor medicine, clinical response to these drugs is reduced due to the emergence of drug resistance as a result of toxic effects in the tumor microenvironment. Research on different types of human cancers has revealed that aberrant expression of miRNAs promotes resistance to the aforementioned drugs. In this study, we review the mechanisms of tumor cell resistance to mAb therapies and the role of miRNAs therein. Emerging treatment strategies combine therapies using innovative miRNA mimics or antagonizers with conventional approaches to maximize outcomes of patients with cancer.     

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities

Background

To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell lines affected with either HPV16 or HPV18 were assayed at 8 sequential time points for gene expression (mRNA) and gene copy number (DNA) using high-resolution microarrays. Available methods for temporal differential expression analysis are not designed for integrative genomic studies.

Results

Here, we present a method that allows for the identification of differential gene expression associated with DNA copy number changes over time. The temporal variation in gene expression is described by a generalized linear mixed model employing low-rank thin-plate splines. Model parameters are estimated with an empirical Bayes procedure, which exploits integrated nested Laplace approximation for fast computation. Iteratively, posteriors of hyperparameters and model parameters are estimated. The empirical Bayes procedure shrinks multiple dispersion-related parameters. Shrinkage leads to more stable estimates of the model parameters, better control of false positives and improvement of reproducibility. In addition, to make estimates of the DNA copy number more stable, model parameters are also estimated in a multivariate way using triplets of features, imposing a spatial prior for the copy number effect.

Conclusion

With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-327) contains supplementary material, which is available to authorized users.     

Online Respondent-Driven Sampling for Studying Contact Patterns Relevant for the Spread of Close-Contact Pathogens: A Pilot Study in Thailand

Background

Information on social interactions is needed to understand the spread of airborne infections through a population. Previous studies mostly collected egocentric information of independent respondents with self-reported information about contacts. Respondent-driven sampling (RDS) is a sampling technique allowing respondents to recruit contacts from their social network. We explored the feasibility of webRDS for studying contact patterns relevant for the spread of respiratory pathogens.

Materials and Methods

We developed a webRDS system for facilitating and tracking recruitment by Facebook and email. One-day diary surveys were conducted by applying webRDS among a convenience sample of Thai students. Students were asked to record numbers of contacts at different settings and self-reported influenza-like-illness symptoms, and to recruit four contacts whom they had met in the previous week. Contacts were asked to do the same to create a network tree of socially connected individuals. Correlations between linked individuals were analysed to investigate assortativity within networks.

Results

We reached up to 6 waves of contacts of initial respondents, using only non-material incentives. Forty-four (23.0%) of the initially approached students recruited one or more contacts. In total 257 persons participated, of which 168 (65.4%) were recruited by others. Facebook was the most popular recruitment option (45.1%). Strong assortative mixing was seen by age, gender and education, indicating a tendency of respondents to connect to contacts with similar characteristics. Random mixing was seen by reported number of daily contacts.

Conclusions

Despite methodological challenges (e.g. clustering among respondents and their contacts), applying RDS provides new insights in mixing patterns relevant for close-contact infections in real-world networks. Such information increases our knowledge of the transmission of respiratory infections within populations and can be used to improve existing modelling approaches. It is worthwhile to further develop and explore webRDS for the detection of clusters of respiratory symptoms in social networks.     

The effect of chronic deafferentation on mental imagery: a case study

Visual- and motor imagery rely primarily on perceptual and motor processes, respectively. In healthy controls, the type of imagery used to solve a task depends on personal preference, task instruction, and task properties. But how does the chronic loss of proprioceptive and tactile sensory inputs from the body periphery influence mental imagery? In a unique case study, we investigated the imagery capabilities of the chronically deafferented patient IW when he was performing a mental rotation task. We found that IW''s motor imagery processes were impaired and that visual imagery processes were enhanced compared to controls. These results suggest that kinaesthetic afferent signals from the body periphery play a crucial role in enabling and maintaining central sensorimotor representations and hence the ability to incorporate kinaesthetic information into the imagery processes.