NEW YORK (GenomeWeb) – The National Institutes of Health this month earmarked more than $1.5 million to fund two projects focused on the roles of specific microRNAs in disease, an effort to profile extracellular RNAs in human biofluids, and the development of a search tool for identifying miRNAs' roles in cancer.
The first grant was awarded to University of Virginia's Brian Annex, a cardiovascular medicine researcher who is investigating the causes and potential treatments of peripheral arterial disease (PAD).
As part of that work, his lab recently reported on the discovery that mice overexpressing miR-93 in hindlimb muscle recovered better from perfusion injury following hindlimb ischemia than normal mice. Notably, recovery was worsened in animals treated with miRNA antagonists. In vitro, miR-93 overexpression attenuated hypoxia-induced apoptosis in endothelial and skeletal muscle cells while enhancing their proliferation.
Hypothesizing that miR-93 plays a key role in boosting angiogenesis, Annex and his team plan to use the NIH funding to uncover how the miRNA improves blood flow following ischemia through gain-of-function and loss-of-function experiments in mouse models of the condition.
The scientists further aim to reveal gene expression changes caused by miR-93 in cell culture, and to examine the miRNA's expression in plasma and skeletal samples from patients with PAD, as well as normal controls.
Annex's grant began on Aug. 1 and runs until June 30, 2018. It is worth $395,000 in the first year.
Also investigating miRNAs in disease is MD Anderson Cancer Center researcher Bisrat Debeb, an oncology professor studying the roles of miRNAs in inflammatory breast cancer (IBC).
As part of his work, he and his team constructed mouse models that, when injected with IBC cells, developed brain metastases at a higher rate than existing xenograft models. Importantly, miR-141 was found to be overexpressed in the animals, and the miRNA's inhibition blocked the spread of the cancer to the brain without affecting lung metastasis.
With the support of the NIH, Debeb and his collaborators hope to confirm their theory that miR-141 mediates brain metastasis, using a range of IBC and non-IBC cell lines, as well as mouse models. They also aim to determine how miR-141 antagonism suppresses brain metastatic colonization and further test the therapeutic potential of the approach in vivo.
The two-year grant project began on Aug. 1 and is worth $208,800 in its first year.
The third grant went to the University of Michigan's Muneesh Tewari, who in 2008 published some of the earliest data showing that miRNAs are present and stable in human plasma, including ones originating in tumors.
Since then, Tewari and others have extensively studied extracellular RNAs (exRNAs), yet more than 95 percent of those found in blood and other biofluids remain uncharacterized, he wrote in his grant's abstract. Further, there have also been reports of diet-derived miRNAs in circulation, although findings from other groups have cast doubt on such studies.
Regardless, "more systematic and comprehensive characterization of blood exRNA is needed," Tewari wrote.
To that end, he and his colleagues plan to analyze unique cohorts of well-defined specimens in order to characterize the spectrum of endogenously and exogenously derived exRNAs in human body fluids. These cohorts will include healthy individuals of matched plasma, urine, and serum identified from an observational and tightly controlled epidemiology study; serial plasma samples collected before and after controlled feeding of vegetables in a study of healthy volunteers; and a cohort of semen specimens from healthy men.
Quality assessment, fractionation of vesicle and non-vesicle-associated fractions, and high-throughput sequencing using multiple library preparation will be performed to capture as many exRNAs as possible, and bioinformatics will be used to annotate both endogenous and potential exogenously derived exRNAs. Lastly, droplet digital PCR technology will be used to validate and provide absolute quantification of exRNAs of interest to help establish reference ranges of exRNA variation in healthy individuals.
The project is set to run for four and a half years, and is worth $661,126 in its first year.
The last grant went to Jingshan Huang of the University of South Alabama, a computer science researcher who specializes in bioinformatics and recently published details of a proposed semi-automated method for miRNA ontology development.
"The manual integration of information on miRNAs and their target genes is challenging — labor-intensive, error-prone, and subject to biologists' prior knowledge because it involves an extremely large amount of heterogeneous data sources to be explored," he wrote in his grant's abstract.
To overcome this challenge, and with the NIH funding, Huang and his team are developing a semantic search tool called OmniSearch that they hope will assist in the efforts to pinpoint the roles of miRNAs in cancer.
The tool will take advantage of OMIT, an ontology that encodes miRNA domain information and is being designed to "formally define miRNA knowledge and will provide a global metadata model as the foundation for automated knowledge acquisition," the abstract states.
OmniSearch will be developed within the OMIT metadata model and is expected to include an automated semantic data annotation and integration tool. The resultant knowledgebase will contain completely machine-readable data integrated from heterogeneous sources including miRNA target prediction databases, Gene Ontology, and PubMed.
The three-year project began on Aug. 1 and is worth $310,864 in the first year.