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Nucleonics Catherine Pachuk on Founding and Guiding an RNAi Company

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Name: Catherine Pachuk

Position: Research associate professor, Thomas Jefferson University/ vice president of biological research, Nucleonics

Background: Associate research fellow, Wyeth — 1998-2000; Research scientist, associate research fellow, Apollon — 1992-1998; Postdoc, SmithKline Beecham — 1989-1992; PhD, molecular virology, University of Pennsylvania — 1988; BS, biology, Marywood University — 1982

With a co-exclusive license to gene- silencing technology discovered while she was working in the private sector, and an interest in transcriptional regulation that extends back to her postdoc years, Catherine Pachuk went on to co-found RNAi drug developer Nucleonics.

Recently, Pachuk took time to speak with RNAi News about launching her own company and where the enterprise is headed.

How did you become involved with RNA interference?

When we were working with DNA vaccines [at Apollon] we observed what is known as the second dose effect — that’s something that’s been observed by people in gene therapy and DNA vaccines. Basically what the second dose effect is, is the inability to get similar levels of expression the second time you give an expression plasmid.

What I’m not able to do is give the specific gene that we were interested in — that is confidential to Wyeth, [which acquired Apollon], but we observed this phenomenon in adult mice. The observation was that when you inject an animal with an expression plasmid, you see expression for a certain period of time and then the expression dwindles down. That loss of expression is not correlated with loss of the expression plasmid in the tissues of the animal.

Even more interesting is after you see the loss of expression, if you inject the animal with that expression plasmid, you see the second dose effect. …

All of our work pointed to the fact that the second dose effect, indeed, was gene silencing.

We looked at everything. We looked to see if it was an age effect with the mice. We thought that maybe as the mice get older, they were less competent to express stuff from an expression vector. We also did the experiment in SCID mice, because we were thinking that maybe this was an immune effect [wherein] we were making an immune response against the encoded antigen.

But in this particular case, we were expressing a mouse gene in a mouse and it was predicted that there wouldn’t be an immune response. What happened was that we saw the same effect in SCID mice, demonstrating that the second dose effect was not an immune response.

The only thing left was a molecular mechanism. What we originally looked for was antisense RNA that was antisense with respect to the messenger RNA of the encoded protein. We found that there was antisense at the level of .2 percent [of] the level of messenger RNA in the tissues of injected mice. Then, we went back and looked to see if any of that antisense RNA was actually duplexed with message, and it was.

What we also observed was when we were losing expression of the expression plasmid, we lost expression of the endogenous gene, as well. That looked very similar to co-suppression. Basically, that’s when we developed the hypothesis that what we were looking at — and RNA interference as a [term] wasn’t even coined yet — was post-transcriptional gene silencing.

Were these findings ever written up?

They were written up and its in a patent that was written up in early 1999 and co-exclusively licensed by Nucleonics from Wyeth.

How does this lead into expressed-interfering RNA?

These vectors were all expression vectors, and if the silencing was indeed mediated by a double-stranded RNA in the mouse model, then it was an expressed double-stranded RNA.

What we did in the next study to demonstrate that expressed double-stranded RNA can induce this effect was to make an expression vector that specifically and efficiently made double-stranded RNA against a particular gene. It was not capable of making any protein. That vector very efficiently and rapidly displayed a similar phenotype, meaning the expression vector was silenced and the endogenous gene was silenced. …

One of the other things about expressed double-stranded RNA that we demonstrated is that when you express it inside a cell, it does not induce the RNA stress response. We looked at 10 different components of the RNA stress response in cell lines that are capable and competent for the RNA stress response.

[Expressed double-stranded RNAs are] unlike synthetic RNA — even the little [synthetic] siRNAs induce the RNA stress response in these cells.

Can you give an overview of how the founding of Nucleonics came about?

We were very interested in spinning off the RNA interference idea. After a lot of thought and discussion with one of the co-founders, [C.] Satishchandran, we decided that the best thing to do was separate from Wyeth, get faculty positions, and start the company.

Since the technology Nucleonics uses is licensed from Wyeth, would that imply that Wyeth might have interest in what Nucleonics is doing? Has there been any discussions about collaborations?

We’re pursuing [collaborations], but I can’t elaborate on it. We’re looking at a couple of different large pharmas.

The first indication Nucelonics is looking at is hepatitis B. Could you talk about that program?

We’re very late in preclinical studies. We’re actually in the [compound] development mode. We expect to file an IND somewhere around the late first quarter of ‘05. Frank Chisari [of the Scripps Research Institute] is exclusively engaged by Nucleonics for collaborating in the RNAi space in his HBV [mouse] models.

We’ve already generated data in those models and we’re also in the development stages. [As for] what it is going to look like, I can’t give specific details, but I can [say] that one of the advantages of using expressed RNA interference is that you can encode multiple sequetopes — it’s like an epitope except it’s a region of the RNA that induces a functional activity. If you look at the antivirals, not just for hepatitis B but if you look at them for HIV and hepatitis C, you get a lot of escape mutants.

A single siRNA, for example, is predicted to act like a small molecule, because all it takes is one mutation and that particular virus would become resistant to the siRNA. It’s been demonstrated to occur in a cell-culture model of polio. But, if you’re expressing the double-stranded RNA, you can express many different sequetopes, really decreasing the likelihood that you’re going to generate viable escape mutants.

The other issue is a regulatory issue: Each siRNA is a separate entity, and is going to be treated as a separate entity by the FDA, meaning that if you’re going to put two different siRNAs in a vial, you need to test the efficacy of each one separately in a clinical trial then put them both together. [This is] very much like peptide vaccines, for example. But if you’re expressing [dsRNAs] from a DNA plasmid, you can weave them all in and you’ve got one drug in the vial.

How’s Nucleonics’ hepatitis C program coming along?

We expect that maybe to be in the area of about five to nine months behind hepatitis B.

What other sort of things are you looking at?

We’re looking at HIV. It’s behind HCV, but we may be pushing that a little more aggressively — it depends on our financing. … It’s going to be a decision that’s made by the board of investors. We haven’t made the decision to move aggressively yet, but it’s been suggested as a possibility. We won’t make that decision until the financing and we get our new board in place.

Can you comment on the financing? [Nucleonics CEO] Bob Towarnicki told me in October that the company is looking to raise as much as $50 million.

What we’re going right now is closing up [financing] and it’s going to be somewhere between $40 million and $50 million. I think we’re probably about four weeks away.

Other than working at Nucleonics, you’re a faculty member at Thomas Jefferson University. What sort of work do you have going on there?

First off, I’m on a leave of absence. Getting the company together really takes a lot of effort. But, I’ve recently received a $1.6 million grant at Nucleonics, and some of the money has been sub-awarded to Thomas Jefferson and to Scripps. (See RNAi News, 10/3/2003).

It’s likely … that once we get funded I will leave Thomas Jefferson, or maybe stay on as an adjunct professor only.

Was starting up a biotech company daunting?

No, because I’d been involved [in business] when I was at Apollon. I helped to write INDs, I went to FDA meetings, I was somewhat involved in the business development and intellectual property side. I’m very heavily involved in the business development side at Nucleonics, but it’s nothing new. If you were at a biotech company before, chances are you’ve had you’re foot in other things besides research.