Tag Archives: biotechnology

RNAi: Yep, Antisense All Over Again

Yesterday, New York Times reporter Andrew Pollack covered the pharmaceutical industry’s recent rush to the lifeboats of the siRNA/RNAi ship:

When RNA interference first electrified biologists several years ago, pharmaceutical companies rushed to harness what looked like a swift and surefire way to develop new drugs.

Billions of dollars later, however, some of those same companies are now losing their enthusiasm for RNAi, as it is called. And that is raising doubts about how quickly, if at all, the Nobel Prize-winning technique for turning off specific genes will yield the promised bounty of innovative medicines.

In particular, Pollack says companies have been spooked by the apparent side-effects of RNAi:

One obstacle is that the double-stranded RNA snippets, perhaps because they do resemble viruses, can wake up certain immune system sentinels and set off an immune response.

Such responses can be an unwelcome side effect in some cases. In other cases, like in treating cancer or infections, an immune response might be welcomed — but might also obscure whether the gene silencing itself is working.

I recall someone else pointing out exactly that problem a couple of years ago. Since I’m obviously on a roll with predictions here, I’ll throw out another one: the last company standing in the RNAi field – probably Alnylam – will soon be able to buy up all of the relevant intellectual property and talent in RNAi at fire-sale prices. They’ll then restructure into a small, lean operation that will eventually make a modest profit with some niche therapies. In other words, they’ll do what Isis did.

Place your bets.

Oxitec: Biotech Geniuses, PR Morons

British biotech company Oxitec is
at it again
:

Some 6000 transgenic mosquitoes developed to help fight dengue were released in Malaysia on 21 December, according to a statement issued by the country’s Institute for Medical Research (IMR) in Kuala Lumpur yesterday. Just like the first releases ever of the mosquitoes, on the Caribbean island of Grand Cayman in 2009 and 2010, the news came as a surprise both to opponents of the insects and to scientists who support them.

As I said in a previous post, I’d classify myself among “scientists who support them,” so I’m chagrined to see that Oxitec still hasn’t figured out the most basic aspects of public relations. Someone needs to tell these guys that there is such a thing as bad publicity, especially when it comes to releasing genetically modified organisms into the wild. Indeed, the Malaysian experiment has given the company another black eye:

[Medical entomologist Bart] Knols worries that surprises such as the releases in Grand Cayman and Malaysia may erode public trust and provide anti-GM groups with ammunition. The two Malaysian groups, for instance, issued a statement yesterday saying they were “shocked … we condemn the apparently secretive manner in which the trials have been conducted.” Helen Wallace of the advocacy group GeneWatch UK says the lack of communication does little to instill confidence in Oxitec.

Oxitec executives respond that they got the necessary permits, so they weren’t doing anything illegal. That’s hardly the point. When you’re blazing a brand-new technological trail, and you know full well that vocal opponents of the new technology are trying to stop you, the only appropriate response is a large-scale public relations campaign. Open the doors to your labs. Call local radio and TV stations and offer to do interviews. Take out an ad in the paper. Run a blog and talk about the schedule for your activities: what you’re doing, where, and why. Be specific, and be impossible to ignore.

It doesn’t matter if your opponents are irrational, uninformed, or driven by their own hidden agendas – all distinct possibilities in this case. If the technology’s foes can credibly assert that you’re doing secret experiments on the public, you lose.

Please, Oxitec, get your PR game together.

Genetically Modified Mosquitoes: Available Now, Apparently

Count me among those surprised by this:

About a year ago, genetically modified (GM) mosquitoes were released into the wild—and they have been flying under the world’s radar screen until last week. On 11 November, British company Oxitec announced that it carried out the world’s first small outdoor trial with transgenic Aedes aegypti mosquitoes in the Caribbean island of Grand Cayman in the fall of 2009, followed by a larger study there last summer.

The trials were designed to test whether such designer mosquitoes could be successfully used to fight wild mosquitoes that transmit diseases like dengue fever. The announcement, made at a press briefing in London, has taken aback opponents of GM mosquitoes and surprised many researchers in the field of genetic control of insect vectors.

Some are questioning why the company stayed mum for so long, calling it a strategic mistake that provides critics of genetic modification with fresh ammunition. “I don’t think they did themselves a favor,” says Bart Knols, a medical entomologist at the University of Amsterdam. “This could well trigger a backlash.”

Knols is absolutely right. The company claims it publicized the trial among island residents (but see the comments after the Science piece for a different take on that). Even if they did have a good local information campaign, they clearly failed to tell the wider world about an experiment that they should have known would be highly controversial. I personally think the benefits of their strategy far outweigh the risks, but doing something like this without a full-blown global PR campaign ahead of time is just asking for trouble.

Halloween Special: Reanimated Livers

Researchers at Wake Forest University’s Institute for Regenerative Medicine have developed a really clever strategy to build new livers. They’ll be presenting their work tomorrow morning at the American Association for the Study of Liver Diseases meeting in Boston:

Our laboratory recently developed a decellularization method able to generate an entire organ scaffold from a whole liver, preserving its vascular network. Preliminary studies showed the possibility to efficiently re-cellularize the bioscaffold using perfusion cell seeding in a bioreactor. However, numerous technical issues remain to be addressed to efficiently deliver primary human liver progenitor cells to generate functional hepatic tissue. The purpose of this study was to investigate the feasibility of generating a bioengineered human liver by re-cellularizing the liver bioscaffold with primary human fetal liver progenitor cells (hFLPCs) and endothelial cells (hECs).

In other words, they developed a technique to suck all of the cells out of a whole animal liver, while leaving the collagen scaffold of the organ intact. Then they tried to repopulate that scaffold with human embryonic liver progenitor cells to build a complete human liver. At least to a first approximation, it worked:

Our results demonstrate the efficient generation of a bioengineered human liver organoid with hFLPCs and hECs using a perfusion cell seeding method in a liver bioscaffold. Hepatic and endothelial tissue functions and cell proliferation were detected with 3D tissue progressive formation in vitro.

The rebuilt livers aren’t quite ready to ship to transplant clinics yet. First, the team will need to confirm that these organs can survive in immunosuppressed animals, and that they’re not harboring any pathogens from the scaffold or cell donors. Nonetheless, it’s a neat approach to a tough problem.

From Biodiesel to … Mycodiesel?

It certainly won’t bring prices at the pump down anytime soon, but a new paper in the journal Microbiology reports an astonishing new talent of certain fungi:


An endophytic fungus,
Gliocladium roseum (NRRL 50072), produced a series of volatile hydrocarbons and hydrocarbon derivatives on an oatmeal-based agar under microaerophilic conditions as analysed by solid-phase micro-extraction (SPME)-GC/MS. As an example, this organism produced an extensive series of the acetic acid esters of straight-chained alkanes including those of pentyl, hexyl, heptyl, octyl, sec-octyl and decyl alcohols. Other hydrocarbons were also produced by this organism, including undecane, 2,6-dimethyl; decane, 3,3,5-trimethyl; cyclohexene, 4-methyl; decane, 3,3,6-trimethyl; and undecane, 4,4-dimethyl.

That ingredient list overlaps significantly with diesel fuel, and the researchers dubbed the fungal brew “myco-diesel.” In an accompanying press release, Montana State University’s Gary Strobel explains that the news gets even better: “We were very excited to discover that G. roseum can digest cellulose. Although the fungus makes less myco-diesel when it feeds on cellulose compared to sugars, new developments in fermentation technology and genetic manipulation could help improve the yield.”

Cellulose is a common agricultural waste product and the Holy Grail of biofuel feedstocks, so finding an organism that can turn cellulose into hydrocarbons directly is big news. Before you rush out to invest in myco-diesel fermentation, though, read the fine print in the research paper; the mycodiesel yields are in the tens of parts per million, so the fungus isn’t exactly gushing crude. Still, it’s off to a promising start.

Antisense All Over Again

Way back in the 1990s, a bunch of biotechnology startup companies charged into a field that promised to be the Next Big Thing in disease treatment: antisense DNA. This mini-boom was driven by the discovery that short segments of DNA could silence genes in cells very specifically. All you had to do was make a DNA oligonucleotide that was complementary to the gene you wanted to silence, and when it got into a cell, it would essentially gum up that gene’s expression. DNA oligos were already trivially easy to make, and gene sequencing was getting cheaper by the day, so antisense promised to usher in a new era of tailor-made medical treatments for everything from cancer to bacterial infections.

Then it all went pear-shape. Someone discovered that these supposedly very specific antisense treatments, some of which were already in clinical trials, were in fact all acting by the same mechanism. Instead of silencing specific genes, it turned out that antisense DNA in the body merely goosed the immune system nonspecifically. What had been touted as a powerful treatment system for a wide range of diseases was in fact just a generalized, and not particularly strong, immune booster.

Practically overnight, dozens of antisense companies went bankrupt as their stocks plunged. The sole survivor of that shakedown, Isis Pharmaceuticals, eventually reconfigured itself to make a few niche therapies, and has done pretty well in the process. All of the others are gone, and most biotechnology investors want nothing to do with antisense anymore.

Just a few years ago, a bunch of biotechnology startup companies started charging into a field that promises to be the Next Big Thing in disease treatment: small interfering RNA, or siRNA. This mini-boom is being driven by the discovery that short segments of RNA can silence genes in cells very specifically. Proponents of siRNA say that their technology is not at all like antisense, and that they’ve done the proper controls to prove it.

Then we get a report like this one. As the researchers explain in the accompanying press release:

siRNAs have been highly touted for their ability to target very specifically and selectively the disease-causing factors in a range of disorders, from viral infections to tumors and inflammatory and immunologic processes. However, siRNA also has the potential to activate innate immunity and the production of interferons, which can in turn bring about therapeutic effects in a range of disease models.

The authors of this paper contend that, “surprisingly few of the reported studies have adequately tested, or controlled, for the potential effects of siRNA-mediated immune stimulation.”

In the current study, use of a commonly used control siRNA sequence called GFP siRNA, which has only a minimal capacity to activate the immune system, clearly showed the striking difference between the immunostimulatory potential of GFP siRNA and of some other siRNAs. Using a mouse model of influenza, the authors demonstrated that the anti-viral activity of siRNA is mainly due to non-specific stimulation of the immune system rather than to a targeted attack on the disease-causing virus.

Is there an echo in here?

The Biogenerics Debate Heats Up

Yesterday’s Chicago Sun-Times brings news that should keep some biotech investors up at night:

Lake Forest-based hospital products maker Hospira Inc. said today it landed European authorization to market the biogeneric anemia drug Retacrit in Europe, making the medicine its first marketed biogeneric medicine.

Hospira said it will launch the product, used to treat anemia in cancer and dialysis patients, in Europe beginning with Germany in early 2008, but Hospira executives said earlier that the drug won’t have an impact on Hospira’s bottom line in the next few years.

Retacrit will compete with Amgen’s cash cow Epogen, which has been off patent for awhile now. Unlike conventional drugs, protein-based therapies like Epogen (recombinant human erythropoietin) haven’t had to face generic competition when their patents end. Biotechnology companies have acted accordingly, keeping the prices of protein-based drugs very high. This loophole exists because biological products have historically been things like plant extracts, which are virtually impossible to quantify and standardize, so regulators in most countries hadn’t contemplated anyone making biologically equivalent copies of these medicines. In Europe, at least, those regulations have now been revised to allow the introduction of “biogenerics,” and Hospira is taking advantage of that.

The US FDA is still debating the issue of biogenerics, and of course the makers of brand-name protein therapies have been lobbying hard to maintain the status quo. If Retacrit takes off in Europe next year, it will give biogenerics proponents more ammunition. I wouldn’t place bets on the final outcome of this fight, but I’m pretty sure it will be a boon to civil litigators in either case.

Genetically Engineered Pests – Coming To a Field Near You?

Entomologically-minded readers of the Federal Register (you know who you are) might have noticed an interesting item shortly before Christmas: in the 19 December issue, the Department of Agriculture posted this note asking for the public’s thoughts about genetically modifying insect pests. Specifically, they’re working on inserting some choice genes into fruit flies and pink bollworms, then releasing the re-engineered critters into the environment. I’m sure the usual naysayers will soon be screaming about Frankenflies (which, by the way, would be a good name for a band), but this project could actually be a tremendous boon to the environment.

Pink bollworm life cycle illustration
Pink bollworm life cycle, image courtesy USDA

The focus of the effort is actually a decades-old insect control strategy called the Sterile Insect Technique, or SIT. Unlike most pest control approaches, SIT has the potential to eradicate an insect species completely, without any harm to non-target species. Somewhat counterintuitively, the first thing you do in SIT is to build a hatchery and start rearing thousands of the insects you want to wipe out. Then you kill the females, and expose the males to some chemical or physical insult that sterilizes (but doesn’t kill) them. Finally, you release the sterile males into the wild, where they mate with females, who then lay clutches of eggs that will never hatch.

Because many insect species mate only once in a season, each sterile male that competes successfully for a mate wipes out one female’s entire reproductive output for the year. The next season’s crop of wild flies will be that much smaller, but you release the same number of sterile males, giving them an even better chance of bedding an otherwise fertile female. After several generations of this, the wild population will go extinct, and you can fold up the hatchery and go home.

It’s a stunningly elegant strategy, and even more impressively, it works. Edward Knipling, the entomologist who invented SIT, proved that 25 years ago, with Cochliomyia hominivorax, the screw worm fly. Screw worm (another good name for a band) gets its common name from a habit of laying its eggs on live animals, letting the maggots burrow into the flesh (like a screw) to feed on blood and develop. After pupating, the adult hatches out of the now-festering wound and flies away. It’s very gross, and very costly; historically, screw worm infestations were an enormous problem for livestock farmers in the Americas, especially cattle ranchers. Using SIT, Knipling and his colleagues eradicated the fly from this country by 1982. It’s since been extirpated from several other countries the same way.

Now the Department of Agriculture is trying make SIT more efficient. Using current technology, SIT programs are damnably expensive, mainly because of the challenges of separating the sexes of tiny insects (can you tell girl bollworms from boy bollworms? ten thousand times a day?), and making sure that the sterilization works just right. Too much radiation or chemical treatment, and you get dead males. Too little, and you get fertile males. Neither is useful for SIT.

Genetic engineering could address both problems. Inserting an inducible gene regulation system that selectively kills females in the larval stage, and another that sterilizes males, would make the breeding program a snap: just induce the genes, grow up the flies, and release whatever survives pupation. One could also get more sophisticated. How about building a paternally-inherited, female-lethal gene expression system into the flies rather than sterilizing them? Males coming out of the hatchery would mate with wild females, who would then lay eggs that would only produce more males – males that would carry the same trait to the next generation. This sort of genetic pesticide, if it worked, could wipe out all of the females in a few generations, and the whole species right after that.

Beyond a few interesting laboratory findings, all of this is theoretical right now, which is exactly why it’s good to see the Department of Agriculture asking for comments on it. Maybe there will be an informed public debate about the risks and potential of this approach. Or maybe there will be a lot of screeching and shouting from various corners, followed by a permanent stalemate that keeps this promising technique on ice.

Hypoallergenic Cats

If you thought the public debate over new genetic technologies couldn’t get any more muddled, just watch what happens as this product starts to show up in pet stores nationwide. Yes, that’s right, hypoallergenic cats. Specifically, they’re cats that don’t express the gene for the most significant feline allergen protein. They are not clones, nor are they genetically modified in the same way many of our crops are these days, but they’re also not quite “natural.” Here’s why these distinctions matter.

The Allerca cat was produced by biotechnology-assisted artificial selection. Like traditional animal breeders, the company identified a desirable trait (lack of the allergen), then crossed animals with that trait, selectively inbreeding the offspring that inherited it. The result was a stable line of domestic cats that don’t produce the allergen. Why was this “biotechnology-assisted?” Because it used molecular techniques to test the animals for the expression of the undesirable gene, something that would have been difficult or impossible just a few years ago.

The strategy is nearly identical to one used in the late 1990s to speed up selective breeding in trees. An Australian company named ForBio, which has since gone out of business, had hoped to select new strains of trees with a range of commercially useful traits, from disease resistance to increased paper pulp production. More efficient technologies for producing transgenic trees made ForBio’s approach a lot less attractive to investors.

That brings me to the kicker: will more efficient genetic modification techniques be developed for cats, and will those supplant the current Allerca artificial selection approach? If so, we should be on our guard for a subtle bait-and-switch. We’ve been artificially selecting cats for thousands of years, and the current Allerca technique is only a minor addition to that time-honored practice. The molecular techniques make it quicker and easier to find the kittens with the right traits, but they don’t enable anything fundamentally new.

Putting in transgenes from other species would be a much more significant change. For example, the green fluorescent protein from a bioluminescent jellyfish can be transferred into mammals to make them glow bright green under ultraviolet lights. It’s unlikely one could ever get that result through selective breeding, and that’s just the tip of the issue.

A substantial increase in the efficiency of feline somatic cell nuclear transfer would be yet another major departure. SCNT can yield a genetically identical copy of an individual, but it can also be used to delete or replace specific genes. Like transgenesis, it enables entirely new classes of genetic modification that could never be done through traditional breeding.

Unfortunately, public discourse on these distinct technologies has already melded into a single pot of rhetorical goo. Once Allerca cats become commonplace, I imagine the genetically modified pet market will be wide open.