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Q&A: NYU's Ramanuj Dasgupta on Running High-Throughput RNAi Screens


Name: Ramanuj Dasgupta
Position: Assistant professor, pharmacology/Director, RNAi Core Facility, New York University School of Medicine
• Postdoc, genetics and developmental biology, Harvard Medical School — 2002-2005
• PhD, developmental biology, University of Chicago — 2002
• BA, genetics, Cambridge University — 1996
• BSc, chemistry, Delhi University — 1994

After completing a postdoctoral stint in the lab of Norbert Perrimon, a key figure in RNAi, Ramanuj Dasgupta moved to New York University, where he researches the Wnt/Wingless signaling pathway in Drosophila.

At NYU, he also helped establish and directs the NYU RNAi core facility, which offers access to high-throughput RNAi screening technologies to researchers from NYU, as well as those from other institutions.

This week, he spoke with RNAi News about the facility, challenges in raising awareness about the potential of high-throughput RNAi screens, and plans for an upcoming RNAi symposium at NYU.

When was the NYU RNAi core facility officially opened?

Officially, it was [opened in] the summer of 2008, but it started off as an extension of my lab in 2007. We've been working on it since 2006, but it took us a while to get everything up and running.

What is the main interest of your lab? You worked with Norbert Perrimon [at Harvard Medical School], so I imagine there is an RNAi component.

I was one of the first to start whole-genome RNAi screens for cell-signaling pathways. And [my lab at NYU] is interested in pretty much every aspect of the Wnt signaling pathway, which is a major signal-transduction cascade involved in numerous aspects of development, as well as disease. [Back when I worked in the Perrimon lab,] our idea was to screen the Drosophila genome using these whole-genome RNAi screens to identify novel inhibitors or activators of the Wnt pathway.

In my lab [at NYU], we are working not just in flies but in mammalian cells. So with the libraries that are available in the [RNAi] facility, we do a lot of cross-species validation of the hits that we get from flies in mammalian cells.

And that work from the Perrimon lab carried over into your lab at NYU?

Exactly. When I came to NYU, the idea was to have a screening facility similar to [the Drosophila RNAi Screening Center at Harvard] since a lot of people here have expressed interest in doing RNAi screens. That was partly why I was hired, as well.

But what I wanted was to have [our facility] slightly different, with all the species represented … under the same roof so that people could go back and forth between species to look for conservation of function of genes.

So what we have at NYU, through a collaboration with Norbert [Perrimon], is the second-generation Drosophila library [co-developed at Harvard and at NYU School of Medicine]. And we are also making subsets for different functional groups [within that library] like transmembrane proteins or transcription factors, kinases, phosphatases, et cetera.

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Then, we have the human whole-genome library that we bought from Ambion. We have the mouse druggable genome, also from Ambion, and we have the C. elegans whole-genome bacterial-feeding library [developed by Julie] Ahringer [at the Wellcome CRC Institute at the University of Cambridge]. We also have human microRNA libraries, both pre-miR [miRNA precursor] and anti-miR [miRNA inhibitor] libraries.

Some of the major success stories [using this kind of RNAi screen resource] are ones where the mammalian cell biologists have optimized their assays in flies, especially in conserved pathways, and found novel genes/modifiers. Then they go back, test them, and find the function is conserved.

At this point, it is about six months after the initial kickoff [of the RNAi core]. What has the response been from the NYU community?

It's been pretty good. We've completed about three screens already, and there are about five in the pipeline. There is also one screen that is supposed to start [this week] from Mount Sinai, which is actually a collaboration with my lab.

People are also optimizing their assays to screen at our facility from [Memorial Sloan-Kettering Cancer Center], Columbia [University] … as well as Albert Einstein College of Medicine. So we're getting a lot of outside requests, and of course [the facility] is open to anybody and everybody.

I think once [these initial] screens are completed and papers are published, then we'll get a lot more visibility from the international community, as well. The model we've based the facility on pretty much is [Harvard's] facility — it's open to anybody and we encourage people from outside to come and do screens.

Are you getting interest from parties out of state?

Out of state, we still haven't. I think we'll have to wait until these papers are published. Even though [information about the NYU RNAi core] is on the web and we've advertised it as much as we can … even at NYU we find people still don't know about it.

A lot of people I've spoken with who run these kinds of facilities have said that one of the biggest challenges is not just getting the word out, but also working with people so that they can figure out how to do their experiments using this kind of technology. Do you find that to be the case?

Absolutely. And most of the people who come with questions are kind of skeptical about whether they will be able to do their kinds of assays in this high-throughput screen format. … They're just not aware of what can be done pretty easily these days in 384-well plates and 96-well plates. Sometimes it's just overwhelming for people who haven't been screening.

I find that especially [to be the case] in New York. In Boston, there is a kind of culture of screening. … There are a lot of people who are screening, and people hear about them … and [discover] that they can easily do this. But here I see so many people who could easily screen —they have fantastic assays — but they have not thought about it that far, they don't know they can actually screen with that assay because they've always done their screens in 10-centimeter 6-well dishes or 12-well dishes, but never in quite a high-throughput format.

Then, of course, there is the other aspect of time and money that you need to spend to optimize an assay in 384-well plates. Once people do have assays and express interest, one thing they sometimes don't spend enough time on is optimizing their assays for 384-well plates.

This facility gives [researchers] all the help it can in terms of advice, and protocols and everything we publish is available on the website, as well. But some people think the facility will do the optimization for them and that's not true; our facility is not a fee-for-service [operation]. People have to come in and do their own screens because they know the biology the best. But we help with all the technical issues with using all the instrumentation and we can give a lot of advice regarding optimizing assays such as transfection, cell lines, concentration of siRNAs, et cetera.

What sort of approaches are you taking when it comes to getting the word out to researchers that they can do these kinds of screens?

At NYU, there are a lot of inter-department seminars and there are floor meetings and fly clubs. By now, a lot of people are coming to me … so there is more and more demand, and people are getting interested in doing screens.

We are [also] planning a major RNAi symposium on February 11 that advertises this [facility]. Norbert [Perrimon] is coming to give a talk, as is Caroline Shamu, who is the director of [the Institute of Chemistry and Cell Biology at Harvard, which runs an RNAi screening facility] and [NYU researcher] Fabio Piano, who has done a lot of screens. Then we have three screeners who have actually screened at our facility who will present their preliminary studies.

That will be a major [initiative] and we'll have fliers all over the New York City institutions. [Raising awareness] outside of New York is kind of tough. I really feel that we need to get some of the papers out [from people] who have used our facility … [which will] pique interest.

As far as you know, is there any resource like this in the New York area?

No. Ours is unique in the sense that it offers multi-species libraries. It's not that there aren't high-throughput screening facilities in the area — [for instance], there are small molecule-screening facilities at Rockefeller [University]. But at all these places, [the facilities] are limited for use to the institutional investigators. It's not open to anybody who is not working at those [places]. So we're unique in terms of being open to everybody.

Is there a website for the symposium you mentioned?

We were planning to put something about it on the news section of our website. The problem is our IT person left … so we are in the process of hiring an IT and bioinformatics person. So there is nothing on the web about the seminar as yet.

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