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Q&A: SBMRI's Mark Mercola on microRNA Screening and Embryogenesis


Mark Mercola

Director, muscle development and regeneration program, Sanford Burnham Medical Research Institute

• Associate professor, cell biology, Harvard Medical School — 1998-2002
• Assistant professor, cell biology, Harvard Medical School — 1991-1997
• PhD, molecular biology, University of California, Los Angeles — 1985
• BA, microbiology, University of California, Los Angeles — 1979

Researchers from the Sanford Burnham Medical Research Institute last month published data from a whole-genome microRNA screen identifying two miRNAs, let-7 and miR-18, as key regulators of germ layer formation during early embryogenesis.

The findings, which appeared in Genes & Development, not only provide new details about germ layer specification, but show the power of such screening experiments in answering complex questions about developmental processes, according to Mark Mercola, the study's senior author.

This week, Gene Silencing News spoke with Mercola about the findings.

Let's start with a little background on you and your lab.

We're interested in heart disease, so everything we've been doing over the last 15 years or so has been to understand the mechanisms we could apply to heart disease. In particular, I want to regenerate the heart or protect it after injury.

Heart failure therapeutics are focused on basically unloading the heart — having it do less work — by reducing pressure in one way or another. What we're trying to do is completely different. We want to rebuild the heart, or protect and maintain its contractility in some way.

What this [latest] project was about was to test the concept that you can screen microRNAs to identify drug targets. The logic is that microRNAs evolved to target particular proteins that control a developmental process. So microRNAs co-evolved with their targets to fine-tune nearly every developmental or pathological process known. By screening a complex process with microRNAs, you can identify the microRNA targets, and those are the targets that nature has shown to be good targets for modulating a process.

What we did was a proof of principle [showing that] if we screened a complex biological process, [in this case, the segregation of mesoderm and endoderm derivatives of mouse embryonic stem cells] against microRNAs, we could identify a pathway that controls that process.

Had you worked with microRNAs before?

We have ... but unlike most people's approaches, which is to look for their expression, we come from the thinking that microRNAs are a very good library of molecules to use to screen in a chemical biology/functional genomics-type approach. In this approach, you screen libraries of molecules, looking for the ones that have an activity, then you figure out how they work. And when you figure out their targets, you've hopefully discovered new targets that control [a process of interest].

With that as a backdrop, can you give a snapshot of the work you did for this latest paper?

We used an embryonic stem cell assay where we differentiated the cells to make either heart [tissue], mesoderm, or endoderm, [which produces gastrointestinal tract and other tissues]. The idea was to screen microRNAs for those that would bias the progenitor [cell's] fate, shifting it to mesoderm or shifting it to endoderm. We came up with two good families of microRNAs that did that: [let-7 and miR-18].

[In this kind of work, miRNAs make] a very good library because the natural logic of microRNAs is that they target multiple proteins. But they've evolved with their targets so that they are particularly interesting proteins. If we just do a random screen of all the proteins in the body, most are not going to be ideal drug targets.

And there was some further validation of let-7 and miR-18 in vivo?

Yes. We took [the miRNAs] in vivo into [mouse] embryos in the relevant [developmental] setting, and we found that if you disrupt the interaction between let-7 and its target, which turns out to be the receptor for the TGF-beta molecule, it shifts the balance between mesoderm and endoderm. [Inhibiting let-7] basically will drive cells from mesoderm and ectoderm into endoderm. [Similarly, miR-18, which was found to down-regulate Smad2, promotes mesoderm at the expense of endoderm.]

That alone was not a great discovery. People have known that TGF-beta signaling is important in that process. … What's important, firstly, is that we could use microRNAs to dissect it, and secondly, those two microRNAs actually fine-tune TGF-beta signaling to establish the border between the tissues.

The real value in what we did is showing that you can go from microRNAs to target, and now, if we were to screen more physiologically relevant assays with this same approach, we could identify key proteins that control those complex processes.

The strength of what we've done is the approach. This was a proof-of-principle screen. A lot of the developmental biologists will get excited about it for what it shows, but for me, what is really important is the fact that we could arrive at the conclusion using microRNA screening.

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