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Rockefeller, OSU miRNA Researchers Pull in Big Bucks Under Recovery Act

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By Doug Macron

With $10 billion in funding under the Obama Administration's $787 billion American Recovery and Reinvestment Act, the National Institutes of Health has already handed out millions to support RNAi- and microRNA-focused research since the legislation was passed in February (see RNAi News, 9/3/2009).

But among those sharing in the more than $29 million in RNAi and non-coding RNA-related grants handed out by the NIH in fiscal 2009 under ARRA, two researchers — Rockefeller University's Sohail Tavazoie and Ohio State University's Carlo Croce — by far brought in the most stimulus money, receiving multi-year awards worth roughly $2.5 million and $2 million, respectively, this year alone.

With his share of the ARRA funding, Tavazoie aims to uncover miRNAs that can be used to predict how a cancer patient will respond to chemotherapy, with a particular focus on colorectal cancer.

"Systemic chemotherapy can prevent metastasis in some patients by killing microscopic tumor cells throughout the body … [and] can also dramatically reduce the size of metastases in some advanced-stage patients," Tavazoie noted in his grant's abstract. Yet, these standard-of-care regimens are "administered to hundreds of thousands of patients without prior knowledge of the sensitivity of individual patients' cancer cells to such treatments.

"If we could identify the chemotherapeutic-responsive and -resistant subsets of patients at diagnosis, innumerable patients would be spared from the risks, side effects, and expense of ineffective chemotherapy and instead offered alternative and experimental therapies in the upfront setting," he wrote. At the same time, such discoveries could "provide mechanistic insights into the molecular underpinnings of chemotherapeutic resistance."

Previously, Tavazoie and colleagues discovered a set of miRNAs whose expression is lost in developing human breast cancer cells, and that restoring expression of these small RNAs in malignant cells suppresses lung and bone metastasis in vivo.

Their work, which was published earlier this year in Nature, also showed that one specific miRNA, miR0335, regulates metastasis and migration of cancer cells by suppressing the expression of the progenitor transcription factor SOX4 and the extracellular matrix protein tenascin C.

Turning his attention onto colorectal cancer, which he notes is "a highly prevalent and aggressive disease entity with significantly fewer treatment options than breast cancer," Tavazoie will use the NIH funding to "apply a conceptually and technically innovative, systematic, and multi-disciplinary approach to discover chemotherapeutic-response predictive microRNAs through an experimental approach that integrates molecular, in vitro, in vivo, and human clinical insights," he wrote in the abstract.

Ultimately, he aims to validate the miRNA biomarkers in prospective human studies that, if successful, could yield an approach applicable to other cancers. "The identification of such microRNAs will not only be of tremendous clinical value now, it will also lay the foundation for future mechanistic and synthetic efforts aimed at generation of novel microRNA-based therapeutic agents for the prevention and treatment of cancer metastasis," he added.

Tavazoie's grant began on Sept. 30 and is set to run until Aug. 31, 2014.

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Croce's grant, meanwhile, centers around how the loss of one specific miRNA can be used as a predictor of a cancer patient's response to demethylating agents.

In earlier work, Croce and colleagues have shown how miR-15a and miR-16-1 are deleted or down-regulated in the majority of cases of chronic lymphocytic leukemia and are both negatively regulate the anti-apoptotic B cell lymphoma 2 protein posttranscriptionally.

They have also demonstrated that over-expression of miR-155 triggers the development of B cell malignancies, possibly through the suppression of SH2-containing inositol phosphatase, as well as roles for the miR-29 family in lung cancer and acute myeloid leukemia.

A pioneer in the miRNA field, Croce has also shown that the miR-29 family directly targets the de novo DNA methyltransferases 3A and 3B, indirectly targets the maintenance DNA methyltransferase 1, and that the loss of members of this family results in over-expression of DNMT3A, 3B, and 1.

"This leads to silencing of tumor suppressors through methylation of CpG islands of their promoters," a process that can be reversed through transfection with miR-29s, Croce noted in his grant's abstract. "Thus, loss of miR-29s and over-expression of DNMTs seem to cause epigenetic changes associated with tumor development."

To take these findings further, Croce is planning to conduct three "small clinical trials to validate that loss of miR-29 is a predictor of response to demethylating agents such as 5-azacytidine and decitabine in lung cancer, AML, and the aggressive form of CLL," according to the abstract. Results from these studies will also be validated in mouse models of the diseases.

"This program will result in major research and development innovations that will effectively be linked to long term improvement and growth in oncology, public health, and health care delivery," he concluded.

Croce's project runs from Sept. 30 until Aug. 31, 2011.

Tip of the ARRA

Though not on the level of Tavazoie or Croce, two other RNAi/miRNA researchers received ARRA awards from the NIH that broke the half-million-dollar mark.

These include Liang Xu from the University of Michigan at Ann Arbor, who secured a two-year grant, worth $614,396 in fiscal 2009, to develop a nanovector system for the delivery of miRNA-based therapeutics to human pancreatic cancer stem cells.

With previous funding from the NIH, Xu and his colleagues developed nanovectors for the delivery of siRNAs and shRNAs targeted to B cell lymphoma cells. "We found unexpectedly that our nanovectors also targeted to pancreatic cancer stem cells," and were able to deliver RNAi molecules to the cancer cells, inhibit their self renewal, and reduce the number of cancer stem cells in vivo, he wrote in the abstract of his latest grant.

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"Based on our exciting new discovery, we propose … to further develop the nanovectors for delivery of miRNA-therapeutics targeting cancer stem cells," he added.

Specifically, Xu will test the nanovectors' ability to deliver the tumor suppressor miR-34 to pancreatic cancer stem cells and restore the miRNA's function in those cells. "Our long-term goal is to develop [the nanovector/miRNA approach] as a novel molecular therapy targeting human cancer stem cells," he added.

His grant runs from Sept. 17 to July 31, 2011.

Harvard University's Norbert Perrimon, meanwhile, was awarded a one-and-a-half year grant, worth $560,686 in its first year, to make a number of improvements to the school's Drosophila RNAi Screening Center, which provides investigators with access to RNAi technology and expertise for their own screening experiments.

Since its establishment in 2003, the center has been "a resounding success," Perrimon noted in his grant's abstract. "In less than three years, 75 applications from 43 different institutions have been approved by the center, 47 screens have been completed, and 11 primary papers detailing the screens have been already published. The vast experience gained during these first years has been instrumental in shaping our view on how to build upon our initial goals and expand the scope and technology of RNAi [high-throughput screening] in Drosophila."

To improve upon this, Perrimon aims to address the off-target effects observed with long dsRNAs through a re-design of the library, which would allow the center to offer two or more dsRNAs to confirm the specificity of RNAi phenotypes.

With the NIH funding, the center will also "implement a number of key improvements to expand the range of functional screens available … [including offering] sub-collections of dsRNAs against a variety of large gene families such as transcription factors or cytoskeletal proteins for more focused screens, and [adding] miRNA and cDNA constructs over-expression libraries for gain of function studies in Drosophila cell-based assays," the abstract states.

The screening center also plans to "address the need of screeners to handle vast amount of data and the challenge to analyze them [with] a major upgrade of our database and [by] developing powerful computational approaches for data analysis and data mining."

Lastly, with the support of the grant, the center plans to offer "two practical solutions" to validate the results of a primary RNAi screen: the ability to perform focused RNAi screens in mammalian cells with siRNAs targeting human orthologs of genes identified in the Drosophila screen, and the generation of custom short hairpin RNA transgenic flies for rapid in vivo validation, the abstract states.

Perrimon's grant runs from Aug. 14 until April 30, 2011.

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