Cambridge, MA-based Alnylam Pharmaceuticals is getting rid of about one-third of its workforce, as it looks to save cash for clinical trials that it hopes will prove the value of its RNA interference drug technology.

Alnylam (NASDAQ: ALNY) said today it’s cutting 33 percent of its staff, as it looks to concentrate its cash reserves on what it believes are its “highest value opportunities” in its pipeline of experimental RNAi drugs. The company didn’t disclose absolute numbers, but it said in its most recent quarterly report that it had 171 employees at the end of September, so if that number is still current, then 56 people are being let go, and about 115 people will remain at the company.

Alnylam has faced deep skepticism among investors in its RNAi platform, after scientists have struggled to effectively deliver the treatments into cells, and Big Pharma companies like Roche, Novartis, and Merck all scaled back their efforts in the field. But Alnylam, still relatively flush with cash from partnerships it struck years ago, has chosen to forge on by internally developing its own RNAi drugs for a group of liver diseases, where delivery is less of a challenge.

“As we effect our ongoing transformation from a platform company to a product company, now is the time to focus our near-term efforts and resources on what we believe to be our highest value opportunities,” said Alnylam CEO John Maraganore, in a statement.

Alnylam said the cuts are expected to save the company $20 million in cash this year. It ended 2011 with about $260 million of cash and investments in the bank, and said it plans next month to disclose its financial forecast for the coming year.

Alnylam has recently released some preliminary data from clinical trials of a couple RNAi programs that it says have emboldened it to push ahead and become a drug developer on its own. The first is for a rare liver disease called TTR amyloidosis, and the second is for high cholesterol, through hitting a biological target known as PCSK9. The company said today that as part of its restructuring, the TTR program, and another for hemophilia, are now its top two clinical priorities.

This isn’t the first time Alnylam has made layoffs. The company cut 25 to 30 percent of its workforce in September 2010 after Novartis ended a collaboration with the company.

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Alnylam Pharmaceuticals has been saying for a while that it needs hard data from clinical trials to prove its skeptics wrong, and today it’s coming out with an early hint of effectiveness with its RNA interference-based treatment for lowering cholesterol.

Cambridge, MA-based Alnylam (NASDAQ: ALNY) is announcing today that it has gotten some encouraging results from a study of 20 patients who got a single shot of Alnylam’s experimental drug called ALN-PCS. This drug, designed to block the activity of a protein known as PCSK9, was able to reduce the protein by an average of 60 percent after four days when given at the highest of five doses studied. That knockdown of the specific protein translated into an average drop of 39 percent in low-density lipoprotein, the so-called “bad” form of cholesterol that clogs arteries and is known to raise people’s risk of heart attack, stroke and death.

The new drug was well-tolerated at a variety of doses, and no one has dropped out of the study because of side effects, although a mild rash was observed in patients on the treatment, the company said. The study is still ongoing, and Alnylam plans to continue examining the safety of higher doses, but the company is communicating the progress before it’s all wrapped up. Preliminary data is being presented today at the Brigham & Women’s Hospital in Boston, and more details are expected to be presented in the first half of 2012, Alnylam said. The company also plans to discuss the results in more detail on a conference call with investors today at 8:30 am Eastern time.

The data is still from the first of three phases of clinical trials normally required for FDA approval, so this drug still has years of rigorous studies to complete if it is ever going to become a new treatment for lowering cholesterol. But the market for cholesterol-lowering drugs was worth $36.4 billion worldwide last year, according to research firm IMS Health, largely because of the huge success of statin drugs. While many of those drugs are losing patents and facing cheap generic rivals, many big biotech and pharma companies (including Amgen and Sanofi) are focusing on a promising new molecular target in PCSK9, which Robert Langreth of Bloomberg News described in a November feature. Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) also has an anti-PCSK9 product in preclinical development with Bristol-Myers Squibb.

Alnylam is wagering that while other companies are focusing on hitting this protein with genetically engineered antibodies, it will have an effective option that works through RNA interference, which specifically silences the RNA that enables the body to make the PCSK9 protein. If Alnylam can continue to show intriguing data from clinical trials (like it did last fall for a rare condition called TTR amyloidosis), it could help revive some of the enthusiasm for RNAi. Excitement for the technique once ran high because of its new ability to molecular targets that have been considered “undruggable” in the past, but enthusiasm has waned in the past couple years as big companies like Roche and Merck have curtailed their RNAi drug development activities.

The data so far for Alnylam’s PCSK9 program is still quite preliminary. Researchers randomly assigned 20 patients with … Next Page »

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New England saw a flurry of life sciences news this week, from venture firms, new startups, and established biotechs.

—Boston-based Avila Therapeutics presented data at the American Society of Hematology from early human trials of its lead cancer drug, AVL-292, which is on track to enter more extensive Phase 2 trials next year. This compound, a so-called covalent drug that bonds tightly to disease-causing proteins to shut down their activity over time, is targeting cancers such as chronic lymphocytic leukemia.

—Alnylam Pharmaceuticals (NASDAQ: ALNY) could be onto something in the field of RNA interference, a technology that has fallen out of favor in the industry, my colleague Luke wrote. The Cambridge, MA-based biotech reported at a scientific meeting last month that one of its experimental RNAi drugs was able to shut down production of a protein that causes a rare and deadly disease called TTR amyloidosis.

—ImmusanT, a new startup working on therapies for celiac disease, inked a $20 million Series A financing from Vatera Healthcare Partners. The Cambridge-based company is developing a vaccine and a diagnostic and monitoring test for the condition, which renders the protein gluten toxic in the body.

—Newton, MA-based AesRx kicked off human trials of its lead drug Aes-103, a treatment for sickle cell disease. A partnership formed with the National Institutes of Health helped the company get this far, after it struggled to raise venture funding.

—Boston-based Ember Therapeutics raised $34 million from Third Rock Ventures to develop drugs that fight obesity by burning off … Next Page »

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Alnylam Pharmaceuticals has been in the doghouse for a while now, as its technology of choice has fallen out of favor in the industry. But while many people have written it off, the Cambridge, MA-based company has started to show hints that it might—just might—be onto something that works against a rare and deadly disease.

The company (NASDAQ: ALNY) reported last month at a scientific meeting that one of its experimental RNA-interference drugs was able to shut down production of a protein that causes a disease called TTR amyloidosis. The findings, from an early-stage clinical trial of 31 patients, marked the first time that Alnylam has been able to show that an RNAi treatment can specifically block a disease-causing protein in human beings.

The potential of RNA interference has electrified scientists for years, because it offers the potential of blocking disease targets inside cells that can’t be effectively halted by conventional small-molecule or larger biotech drugs. But the excitement has faded the past couple years, as researchers have struggled to deliver these RNA-silencing molecules into cells, and major companies like Roche, Merck, and Novartis have cut back on their investments in the field. Through it all, Alnylam CEO John Maraganore has insisted that the only way to overcome the doubters is to deliver convincing proof from clinical trials, not just mouse or monkey experiments.

Alnylam has made some headway in the clinic the past couple years, and while it’s too early to say it has proved the skeptics wrong, it’s moving full steam ahead on this new flagship program, betting that it will prove that RNAi will someday live up to its promise.

“The level of confidence for us at Alnylam, and among our collaborators, has gone up enormously as a result of this data,” Maraganore says.

Based on the clinical findings (which I’ll get to in a minute), the company has raced ahead with a more potent-second generation delivery technology of its TTR drug, which it plans to move into its first clinical trial in early 2012. The plan is then to move ahead at breakneck speed by wrapping up that study before year’s end, starting a mid-stage study later in 2012, and then leaping all the way into the third and final phase of clinical trials normally required for FDA approval in 2013, Maraganore says.

There are scientific and business reasons why Alnylam has honed in on TTR to be its flagship program. The disease, transthyretin (TTR) amyloidosis, allows excessive amounts of amyloid proteins to build up in tissues throughout the body. Alnylam likes going after this disease partly because … Next Page »

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Marina Biotech has found a way to extend its runway a little longer, by finding a single investor willing to pump in another $15 million.

The Bothell, WA-based company (NASDAQ: MRNA), the developer of RNA interference drugs, said today in a regulatory filing that Lincoln Park Capital Fund has agreed to invest as much as $15 million over the next 30 months in Marina Biotech. The company said it will control the timing and amount of shares sold to Lincoln Park, which will be based on the market prices at the time. Marina has agreed to sell a maximum of 17.9 million new shares to the firm, according to the filing. Lincoln Park has no right to acquire Marina, according to a company statement.

“LPC has participated in the past as an institutional investor in Marina and we look forward to working with them as a financial partner,” said Michael French, Marina’s CEO, in a statement. “This commitment by LPC provides additional financial flexibility as we continue our research and development efforts.”

Getting access to that new line of cash will help Marina buy a little more time when its cash has been running low, during a bleak period for RNA interference companies. Marina had just $5.9 million in cash left at the end of June, according to its most recent quarterly report. In the same quarter, the company had a net loss of $3.6 million. Early in September, Marina said its chief financial officer and chief scientific officer were both stepping down as part of a broader reshuffling of management responsibilities. The company’s slim cash position at the end of the second quarter prompted Marina’s auditor to issue an opinion raising doubts about the company’s ability to continue as a “going concern.” Earlier this month, the company said it was able to terminate the lease on one of its buildings in Bothell in order to preserve cash.

Shares of Marina rose 5 cents, to 19 cents, after the deal was announced.

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We saw a mix of personnel, drug partnership, and acquisition news from New England’s life sciences players this week.

—Atrium Medical, a Hudson, NH-based developer of cardiology and radiology medical devices, is getting acquired by the Swedish firm, Getinge Group, for $680 million. Atrium will act as an independent business unit of the Getinge subsidiary Maquet Cardiovascular.

—Cambridge, MA-based Agios Pharmaceuticals, a developer of tumor-starving drugs, took in another $20 million for extending an exclusive drug collaboration it inked with Celgene last year. Celgene could also pay up to $120 million in milestones for each drug it licenses for its own internal pipeline and further development. That all comes on top of the $130 million Agios earned in upfront payment in April 2010.

—Xconomy national biotech editor Luke Timmerman moderated a live chat on Twitter with John Maraganore, CEO of Cambridge-based Alnylam Pharmaceuticals, on the subejct of RNA interference. “RNAi vs iPhone, RNAi better for patients” is among Maraganore’s pithy tweets that resulted.

—Michigan-based biopharmaceutical company Lycera announced it had hired new CEO Kathleen Metters, who will primarily work out of Cambridge. Metters, a Merck veteran, will oversee Lycera as it enters clinical trials of its drugs for treating autoimmune disease, which will likely begin in 2012.

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Who says you can’t be smart, witty, or say anything of substance in 140 characters or less? Alnylam Pharmaceuticals CEO John Maraganore had a zinger ready yesterday as Apple’s dog-and-pony show was happening during the first Xconomy “Tweetchat,” on the latest ups and downs in RNA interference.

“RNAi vs iPhone, RNAi better for patients” is what Maraganore wrote under the @alnylam Twitter account.

Touche. That was one of the fun comments that were going back and forth in a 30-minute Q&A session that I moderated on Twitter with Maraganore. This event seemed to be quite popular. We had 26 people who either threw some questions at Maraganore during the 30-minute period, or signaled they were following the conversation by notifying their networks of followers about the searchable hash tag #RNAichat. Here’s who joined the conversation, with a little on their background according to their self-described bios on Twitter.

@adamfeuerstein (Adam Feuerstein, Sr. columnist for the TheStreet)

@biotechcfo (Daniel Davis, director life sciences & technology at AMS)

@Chris_Evelo (Chris Evelo, Head of the Department of Bioinformatics – BiGCaT at Maastricht University in the Netherlands)

@JohnCFierce (John Carroll, editor in chief, FierceBiotech)

@bio1x1 (Bio 1×1 Partnering, based in Washington DC)

@corytromblee (Cory Tromblee, life sciences communications pro)

@JohnJSeng (John Seng, founder and president of Spectrum)

@tweetingbiotech (Jennifer Conrad, Sr. account executive at MacDougall Biomedical Communications)

@scientre (Laura Strong, president of Madison, WI-based Quintessence Biosciences)

@illuminatethis (Amber Harloff)

@outlinescience (Mawethu Bilibana, Blogger, Professional student (PhD Chemistry) at UWC and NGO non-executive in Cape Town, South Africa)

@sjohnson7808 (Steve Johnson)

@claytoncomm (Cynthia Clayton, communications, Alnylam)

@biotechben (Benjamin Navon, Biotech, life sciences, and healthcare PR pro)

@bioduediligence (PhD scientist and biotechnology stock investor)

@IBT_Bioservices (IBT Bioservices is a collaborative research organization offering R&D services to identify vaccines and therapeutics with anti-infective activity)

@roseanneseguin (Montreal, Quebec)

@bradloncar (Private investor)

@Michael_Gilman (Scientist and entrepreneur. Founder/CEO of @Stromedix)

@alalejandro (Adriana Alejandro, scientific consultant)

@LifeSciVC (Bruce Booth, early stage VC, recovering scientist)

@brownerM9 (Michelle Browner, CEO of Enlight Biosciences)

@microryza (Fun Guy)

@MelissaLerch (Melissa Lerch, Scientist passionate about global health, infectious disease, science communication, travel, and life)

@Robert_Overell (Robert Overell, CEO of PhaseRx)

@kevinccc (Kevin Colwill, individual biotech investor)

There were lots of good questions, and amazingly, Maraganore was able to keep up and answer all of them as far as I could tell. I personally fired away with these questions:

1. John, why do you think so many people have soured on RNAi? Roche, Merck are a couple big cos that have walked away. Maraganore’s response: “people/companies are waiting for clinical data, which is what we are focused on.”

2. Skeptics seem really dug in against RNAi. What clinical data at @alnylam could change minds? The reply: “silencing of human genes involved in disease is a good 1st step.”

3. Alnylam just moved a cholesterol-lowering PCSK9 drug into clinic. That will cost $. Competitive space. Why do? Answer: “PCSK9 is hottest target in mol. medicine, competition 2b expected; our mechanism only 1 to phenocopy human genetics.”

What really got me even more excited about this event was how this got more people involved. The Tweetchat makes this more like a press conference or an investor breakout session, where anyone with a question can chime in. Here were a few examples, and answers.

From @scientre “Will clinical POC need to be in disease where delivery very general (beyond eye, liver) before skeptics get on board?” Maraganore’s answer: “re: clinical POC; liver is huge win for field & creates opportunities 4 lots of meaningful drugs.”

From @sjohnson7808 “Reasons/causes of liposome induced inflammation been figured out?” The response from Alnylam’s CEO: “re: liposome inflammation; high doses >1mg/kg are pro-inflammatory. our new LNPs silence genes at <0.05mg/kg”

From @BiotechBen “Obviously it takes time bringing a new class of therapies to market, but what do you say to investors who have lost patience?” Maraganore’s response: “re: investors; market has tendency 2 initially undervalue promising new techs, we think clin data could make impact.”

From @IBT_Bioservices “@ldtimmerman @alnylam Curious to know his predictions on RNAi to treat/prevent viral infections. Two minutes later, Maraganore said “re: RNAi viral infections; we are doing Ph 2b study in RSV infection & @RegulusRx doing work on HCV w. miR-122.”

Nothing that Maraganore said was really earth-shaking news. But I got a number of positive comments from folks whose only complaint was that it was too short at just 30 minutes. Maraganore was a good sport about it. Afterward, he said in an e-mail, “It was fun for sure!”

If you have other suggestions of interesting life sciences topics and speakers that we might want to put together for future Tweetchats, just send me a note via e-mail. I’ve already gotten one pretty good tip today from @PearlF (Pearl Freier, Founder of Cambridge BioPartners). See you around in the Twittersphere.

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Marina Biotech, the developer of RNA interference drugs, has been running low on cash for a while, and now it has found a way to send less cash every month to its landlord.

The Bothell, WA-based biotech company (NASDAQ: MRNA) said today in a regulatory filing that it has terminated the lease on its lab and office building at 3450 Monte Villa Parkway in Bothell, and that it has 30 days to clear out, according to a regulatory filing. The company got out of its lease by agreeing to pay entities affiliated with its landlord, BioMed Realty Trust, 7.8 million newly issued shares of its stock at a settlement price of 23 cents a share. The building was previously the home of small-scale manufacturing for nasal spray formulations of drugs, back when the company concentrated on those compounds and was called Nastech Pharmaceutical.

Marina, which now works on RNA-based drugs that seek to specifically shut down certain disease-related genes, will remain in its corporate headquarters down the street at 3830 Monte Villa Parkway, CEO Michael French said. At one point in late 2007, Nastech had about 230 people spread between the two buildings on Monte Villa Parkway. But the 3450 building has been empty for more than three years since Marina shifted its focus away from the nasal spray drug business.

“We’ve finally been able to jettison that ‘legacy’ building,” French said in an e-mail.

Marina has had numerous cash crunches before, but getting rid of that extra building will help Marina buy at least a little more time during a bleak period for RNA interference companies, as major pharma companies like Merck and Roche have backed away from some of their bold RNAi initiatives. Marina had just $5.9 million in cash left at the end of June, in its most recent quarterly report. In the same quarter, the company had a net loss of $3.6 million. Early in September, Marina said its chief financial officer and chief scientific officer were both stepping down as part of a broader reshuffling of management responsibilities. The company’s slim cash position prompted Marina’s auditor to issue a formal opinion raising doubts about the company’s ability to continue as a “going concern.”

Shares of Marina closed at 16 cents today, giving it a market value of about $12.7 million.

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Here’s just a quick reminder that we’re doing the live Tweetchat today with Alnylam Pharmaceuticals CEO John Maraganore. This chat, which anyone with a Twitter account is free to join, will be held today at 1 pm Eastern/10 am Pacific. The best way to follow the questions and answers will be to follow the live stream of questions and answers on Twitter at #RNAichat. I will be asking questions from my account (@ldtimmerman) while Maraganore will be offering up answers at @alnylam.

Anyone else on Twitter who like to send in a question about the latest ups and downs in RNA interference is welcome to fire away at #RNAichat, sort of like how people do at a press conference or an investor breakout session. For those of you who don’t have Twitter accounts, but would like to see how a real-time online chat unfolds, you can see it here at this post on Xconomy. Those of you who aren’t on Twitter who would like to send a question in to Maraganore can just send me an e-mail at ltimmerman@xconomy.com.

This is an experiment of sorts that we’re trying, which I hope will be a fun and informative way to expand the conversation online in biotech. See you here at 1 pm Eastern/10 am Pacific.

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This week’s New England life sciences news spanned companies targeting cancer, schizophrenia, sleep improvement, and genomic analysis.

—Newton, MA-based health IT startup Zeo announced it added a mobile app version of its sleep tracking and coaching system. The company hopes the tool, which pushes sleep data gathered from a sensor-laden headband to a user’s mobile interface, can be integrated with other apps focused on improving wellness.

—RXi Pharmaceuticals (NASDAQ: RXII) of Worcester, MA, announced that it will divide its work on RNA therapeutics from other pursuits, by splitting up into two publicly traded companies. Galena Biopharma, one of the companies, will pursue cancer treatments, while RXi will continue work in RNA interference—molecules that silence disease-causing genes—through developing RXI-109, its drug candidate for treating fibrosis and scarring.

—Boston-based Acetylon Pharmaceuticals, a biotech startup backed by the holding group of New England Patriots owner Robert Kraft, started a human trial of one of its cancer drugs (ACY-1215) that fights the disease by targeting enzymes related to gene expression.

—Karuna Pharmaceuticals, a startup incubated at Boston’s PureTech Ventures and led by ex-Pfizer exec Ed Harrigan, announced it had licensed a group of experimental schizophrenia drugs from Nashville-based Vanderbilt University. The compounds are believed to treat schizophrenia symptoms such as memory loss and the inability to experience pleasure or to carry on normal social interactions, which aren’t currently addressed on the market.

—Cambridge, MA-based Knome is expanding its genomics analysis businesses beyond the mega-wealthy, by targeting researchers in bioinformatics and other fields, my colleague Luke wrote.

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We had an unusual mix of headlines this week on RNA interference, biofuels, and a quiet little startup in Bothell with Icos pedigree.

—There weren’t any major life science company financings to report this week, but the state’s academic centers had something to crow about with $80 million in new federal grants going to the University of Washington and Washington State University. The money is intended to help scientists find ways to turn lots of our regional biomass into renewable fuels, and hopefully create a few jobs along the way.

—I’m trying an experiment next week with a “Tweetchat” with one of the industry leaders in the field of RNA interference—John Maraganore of Cambridge, MA-based Alnylam Pharmaceuticals. For those of you interested in RNAi, and who have Twitter accounts, this will be a good opportunity. It will start at 10 am Pacific on October 4th, and go for about 30 minutes. The idea is to have an open conversation about where this whole gene-silencing business is going after a series of well-documented setbacks. For those of you not on Twitter, but interested in sending a question in to Maraganore, shoot me an e-mail. There is no shortage of interest in RNAi here in the Northwest, with Seattle-based PhaseRx, Bothell, WA-based Marina Biotech, Vancouver, BC-based Tekmira Pharmaceuticals, Vancouver, BC-based Alcana Therapeutics, and Seattle-based Groove Biopharma all working on various pieces of the puzzle.

—Cocrystal Discovery, led by a couple former Icosahedrons in Gary Wilcox and Sam Lee, has kept a pretty low profile its first three years in business. But that’s starting to change now that this company struck a new partnership with Israel-based Teva Pharmaceutical, and Wilcox gave me the inside scoop on what this team is setting out to do with antiviral drugs against hepatitis C, flu, and more.

—Adaptive TCR, a spinoff from the Fred Hutchinson Cancer Research Center, named a few familiar local biotech names to its roster of various advisors. Lee Huntsman of the Life Sciences Discovery Fund has joined Adaptive’s board of directors; Cassian Yee of the Hutch has been added to the scientific advisory board; and Carol Gallagher (formerly of Calistoga Pharmaceuticals) and Stewart Parker of the Infectious Disease Research Institute have been named to the startup’s corporate advisory board. Adaptive, for those just tuning in to this story, is using the tools of modern DNA sequencing and computing to help scientists better understand how DNA get shuffled around in B and T cells that make up our adaptive immune systems.

—We had a lot of perspective this week on what it’s like for women in biotech—not something I’ve written much about here the past three years. This week in BioBeat I talked about what looks like a potent new force for closing the gender gap in biotech—a new all-female networking group called Women in Bio. Coincidentally, we also had a guest post from Lisa Suennen, a venture capitalist in San Francisco, who talked about another women-dominated biotech event she recently attended in the Bay Area.

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Usually when I want to chat with someone, I still pick up that 19th century contraption called the telephone or sometimes meet in person. Each of those communications methods has its merits, but you can bring a lot more voices to a conversation through a real-time chat like the ones happening now on Twitter.

So now I’m getting ready to moderate what should be an informative and fun live chat on Twitter about a hot current topic in biotech—the future of RNA interference technology. I’m happy to say that one of the industry’s leaders, Alnylam Pharmaceuticals CEO John Maraganore, has agreed to take the plunge online and field questions from me, and anybody else who wants to join.

Here are the basics. This free and open chat will start at 1 pm Eastern/10 am Pacific on Tuesday October 4th, and will go for about 30 minutes. For those of you familiar with Twitter, I’ll be sending off short questions from my personal account—@ldtimmerman and from @xconomy. Maraganore, alas, doesn’t yet have his own personal account. But he will be on hand to answer questions in real-time from his company’s account—@alnylam, with some help from Alnylam’s communications director, Cynthia Clayton @claytoncomm. We will keep track of the running dialogue of questions and answers in a single column under the hash tag #RNAichat.

For those readers out there who haven’t yet signed up for Twitter accounts, we’re going to set up a livestream on Xconomy where you can watch the back-and-forth. And, if you’re not on Twitter but would like to pass a question to Maraganore, I’m giving you an out. You can send me the question at ltimmerman@xconomy.com and I’ll put it out there for Maraganore to answer on Twitter. But I will want to identify you and your company, since that’s the way it would appear if you were asking the question yourself.

I haven’t yet figured out exactly what I want to ask yet, but I do know there has been plenty to talk about lately in RNAi. For those of you less familiar, RNA interference has electrified scientists for several years, and its co-discoverers won the Nobel Prize in 2006. The excitement comes from the technology’s potential to hit biological targets of disease that are currently inaccessible by conventional small-molecules or larger biotech drugs. The pharmaceutical industry wrote some very big checks to the emerging biotech companies in the space for a while, although in recent years companies have run into tough technical challenges with delivering these new RNAi molecules where they need to go in cells. Merck and Roche are a couple of the high-profile pharma companies that have made significant cuts in the past year. Just this past week, Worcester, MA-based RXi Pharmaceuticals (NASDAQ: RXII) split into two companies as investors have lost interest, or patience, in its strategy to come up with useful RNAi drugs.

Maraganore has heard the chorus of skeptics for some time now, yet his company continues to forge ahead in what he has proclaimed will be the “RNA decade.” This week, Alnylam (NASDAQ: ALNY) advanced into clinical trials with a novel RNAi drug for lowering cholesterol in patients with severely high cholesterol scores. It is the company’s fourth experimental drug program to advance in clinical trials. Want to ask him why? Or why he’s kept the faith when others have walked away? That should be pretty easy to do in 140 characters or less. See you online at 1 pm Eastern/ 10 am Pacific on Oct. 4.

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[Updated: 8:45 am PT, 9/8/11] Bothell, WA-based Marina Biotech (NASDAQ: MRNA), the developer of RNA interference drugs, has been struggling to hold on during a period when many drug companies have given up on its technology, and today it’s seeing whether a bunch of new blood in the executive suite can help turn things around.

Marina, which had just $5.9 million of cash left on June 30 in its most recent quarterly report, said today that its chief financial officer and chief scientific officer are both stepping aside. CFO Pete Garcia has resigned, and CSO Barry Polisky has traded in that title for a role as “distinguished scientist” and chair of the company’s scientific advisory board.

At the same time, a few new faces are taking on bigger roles at Marina. Richard Ho, the former senior medical director at Foster City, CA-based Entelos, has joined Marina as executive vice president of R&D; Philip Ranker, the former CFO of San Diego-based Suneva Medical will be Marina’s interim finance chief; Alan Dunton has been brought in as consulting chief medical officer; and Michael Templin has been promoted to chief technology officer. CEO Michael French is still the CEO.

[Updated info on salaries] Ho, the new head of R&D, will start his job at an annual base salary of $300,000, get a $90,000 relocation bonus, and get a $30,000 bonus on April 1, 2012 if he successfully integrates and restructures Marina’s research operations, according to a regulatory filing. Polisky, whose role is being reduced to part time, has had his annual base salary reduced to $135,000. Ranker, the new finance chief, will be paid a $275,000 annual base salary, and get $18,000 for relocation.

No official reason was given for all the executive shuffling, but it’s clear that Marina needs to raise some money, and fast. The company had a net loss of $3.6 million in the second quarter, according to its most recent quarterly report, and its slim cash cushion prompted Marina’s auditor to issue a formal opinion raising doubts about the company’s ability to continue as a “going concern.”

RNA interference, a technology in which researchers seek to silence specific disease-related genes in ways that traditional drugs can’t, has excited scientists for years. But no FDA approved drugs have resulted from this line of research, and Big Pharma companies like Roche and Merck have both cast doubts on the field in the past year as they cut back their RNAi efforts.

Marina Biotech shares closed at 22 cents today, down from their 52-week high of $2.91. The company’s market valuation is now about $17.8 million.

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Bothell, WA-based AVI Biopharma (NASDAQ: AVII) said today it has started dosing patients in a mid-stage trial of eteplirsen, an experimental RNA-based therapy for Duchenne Muscular Dystrophy. The study is expected to enroll 12 patients at Nationwide Children’s Hospital in Columbus, OH. Patients will get once-weekly intravenous infusions of the new drug, or a placebo, for 24 weeks, AVI said.

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If you dared to flip the channel to CNBC any time during the past week, it would have been hard to stay calm. The market was whipsawing all over the place, up one minute, down the next. Fear of government defaults and the potential for another recession were topics of endless debate. Fund managers were said to be antsy to unload any security riskier than a T-bill or gold—which means biotech was fast becoming especially unfashionable.

All the fearful talk may have been good for TV ratings and Internet page views. The wave of selling is definitely worrisome for any company that dares to do something risky like create innovative new life science products, such as cancer drugs. But all this talk is hardly a sign of any long-term catastrophe.

The last time I can remember this much fear coursing through the markets was September 2008, when the Lehman Brothers bankruptcy triggered government bailouts to stave off a global run on the bank. Most comments I heard and read last week said what’s happening today isn’t as frightening as that scenario. There are undoubtedly major problems today, like the rising cost of healthcare and the long-term threat that poses to governments around the world. Healthcare investors with any vision at all have to be worried about what might be done to clamp down on costs (and future profit margins) of pharmaceutical, medical device, and diagnostics companies.

Setting aside all those concerns for a moment, I thought it would be instructive to check on how biotech investors reacted during that scary time of September 2008, compared with what we’ve seen the last two weeks. So I looked at the two-week period starting with the close on Sept. 12, 2008 (the last day of trading before the Lehman bankruptcy), and the two-week period starting with the close on Aug. 1, 2011 (the last full day before President Obama signed the bill to raise the debt ceiling, averting what could have been a U.S. government default).

Here’s what I found:

Indexes                                       Sept 12-26, 2008                           August 1-12, 2011

Nasdaq Biotech Index (NBI)               -0.2%                                               -8.6%

Amex Biotech Index (BTK)                 -0.6%                                              -15.1%

Nasdaq Composite Index                   -3.5%                                                -8.6%

Surprisingly, even though most analysts agree the global financial system isn’t in as much trouble now as it was in 2008, biotech indexes, and the broader Nasdaq Composite Index, are getting hit even harder now.

Sure, lots of things have changed … Next Page »

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San Diego’s life sciences community was teeming with news over the past week. We’ve got it all cultivated for you.

—Shares of San Diego’s Adventrx Pharmaceuticals (NYSE Amex: ANX) plunged by more than 55 percent after the biotech company said the FDA refused to approve its new lung-cancer drug vinorelbine injectable emulsion (Exelbine) until a key bio-equivalence trial is repeated. Adventrx CEO Brian Culley has said the company has enough capital to shift its focus to other drugs in its pipeline.

—Qualcomm’s (NASDAQ: QCOM) wireless health team hit the halfway mark today in an eight-week fitness challenge that has equipped 32 employees with wireless monitors and weight scales to help increase their activity and lose weight. I posted a Q&A with Qualcomm’s Don Jones, who also posted this update today on the Qualcomm blog. A Qualcomm spokesman tells me the 32 participants have burned a total of roughly 1.9 million calories and lost a total of 48.5 pounds.

—Pfizer added UC San Diego Health Sciences to its network of drug discovery innovation centers that includes prominent research institutions in Boston, New York, and San Francisco. UC San Diego Health Sciences’ partnership agreement with Pfizer could be worth as much as $50 million over the next five years.

—The La Jolla Institute for Allergy & Immunology officially opened a new center today that is focused on RNA interference technology, and is intended to operate as a collaborative and open resource for the scientific community in San Diego and elsewhere. The RNAi Center was funded by a $12.6 million grant from the National Institutes of Health. If scientists make discoveries of potential clinical benefit, “the natural next step would be to seek partnering opportunities for clinical translation and potential drug development,” said Steve Wilson, the center’s executive director and chief technology officer.

—Former SKY MobileMedia CEO Naser Partovi introduced a year-old startup that provides outpatient management software called Wellaho. Partovi told me that Wellaho operates a HIPAA-compliant social media network around the chronically ill, and which is tailored to the needs of that patient. “You can’t just join Wellaho,” Partovi says. “It must be prescribed for you by your doctor.”

—San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN) and Japan’s Takeda Pharmaceuticals said they are halting further development of pramlintide/metreleptin for the treatment of obesity. Their program was in mid-stage development as a … Next Page »

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Merck has decided to close down the RNA interference research facility it obtained through its $1.1 billion acquisition five years ago of San Francisco-based Sirna Therapeutics, the company said late today.

About 50 jobs are being eliminated, while about 10 people are being offered transfers to other Merck (NYSE: MRK) facilities on the East Coast and in Palo Alto, CA, says company spokesman Ian McConnell. The company still plans to utilize the RNAi technology it got via the Sirna acquisition throughout its global R&D operation, he says. Employees in San Francisco, at the facility at 1700 Owens Street in Mission Bay, were told about the shutdown today, McConnell says.

“We continue to invest significantly in the RNA research field, which we believe represents a potentially transformative technology,” McConnell says. “It’s a difficult decision,” he adds, explaining that it was driven by the company’s need to cut costs.

Merck’s acquisition of Sirna raised eyebrows across the industry from the beginning, because of the high price tag, and the early-stage nature of RNAi technology. This technology has electrified scientists for several years, because it offers the potential of hitting biological targets of disease that are currently inaccessible by conventional small-molecules or larger biotech drugs. Merck paid what many considered to be the lavish sum of $1.1 billion to acquire Sirna, one of the first movers in RNAi.

Since then, Merck hasn’t pointed to any RNAi-based drugs that have emerged in its pipeline, and it has publicly emphasized the challenge it has faced finding ways to effectively deliver these drugs in the body. Merck’s decision comes just a few months after fellow pharma giant Roche pulled out of a high-profile RNAi collaboration with Cambridge, MA-based Alnylam Pharmaceuticals (NASDAQ: ALNY). There are no such RNAi-based drugs approved yet by the FDA for sale in the U.S.

Still, McConnell said Merck plans to continue to use the RNAi technology to help screen drug candidates, an effort which Merck vice president Alan Sachs described in an exclusive interview with Xconomy in January 2010. The RNA group at Merck is now headed up by Jeremy Caldwell, McConnell says.

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We saw several headlines surrounding clinical development by New England-area drugmakers this week.

—Weston, MA-based Biogen Idec (NASDAQ: BIIB) said that it nabbed a conditional approval from the European Commission to market a long-acting version of fampridine (Fampyra) to adult patients with multiple sclerosis who have walking disability. The agency has also asked Biogen to commission a study exploring the benefits, beyond improved walking speed, of the therapy—which Biogen said it had planned to do post-marketing.

—Xconomy East Coast biotechnology editor Arlene Weintraub wrote about how Watertown, MA-based EnVivo Pharmaceuticals is charging ahead with development of its Alzheimers drug—despite negative data reported by Eli Lilly in a drug trial of its own similar compound. EnVivo began Phase 1 testing on June 1 of its compound, EVP-0962, which reduced brain inflammation caused by Alzheimer’s, reversed behavioral defects, and appeared to have a better safety profile than gamma secretase inhibitors (which the Lilly drug is), during animal trials.

—Also perserverent, Cerulean Pharmaceuticals of Cambridge, MA, is pushing ahead with its nanotechnology for drug delivery. The company began a trial this month of its cancer nanoparticle drug and is also continuing development of its technology for the field of RNA interference—which has struggled to realize its potential in the form of successful drugs.

—Natick, MA-based Boston Scientific (NASDAQ: BSX) announced second-quarter sales of nearly $2 billion and earnings of $.17 per share—beating Wall Street predictions by about a dime. The medical devices firm also announced plans to repurchase $1 billion of its common shares and (the day before its earnings announcement) revealed that it will be investing $150 million over five years in a manufacturing facility in China and will be upping its employee head count in the country.

—San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN) and Waltham, MA-based Alkermes (NASDAQ: ALKS) resubmitted their application for the FDA’s approval to market their drug exenatide once-weekly (Bydureon) as a new treatment for diabetes in the U.S. The FDA, which had previously asked the two biotechs to submit data indicating the drug doesn’t have an effect on abnormal heart rhythms known as the QT interval, will have about six months to review the application.

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Chris Garabedian took his first shot at being a CEO last December. Immediately, people thought this was a little bit crazy.

Friends wondered, why leave a job as an up-and-coming VP of corporate strategy at a biotech powerhouse like Summit, NJ-based Celgene (NASDAQ: CELG) to run an obscure little company like AVI Biopharma (NASDAQ: AVII)? AVI was built on a technology, antisense drugs, that few people in the industry believe in. The company’s track record is brutal—30 years spent on R&D with no FDA-approved drug to show for it. There was a leadership void, since a shareholder rebellion led to the ouster of the previous CEO. And, with labs in Corvallis, OR and headquarters in Bothell, WA, it’s a long way off the beaten path for most biotech industry executives and investors.

Garabedian, 44, admits he was skeptical at first. But when encouraged to take a look a year ago by the company’s largest investor, George Haywood, he looked. And the more Garabedian studied, the more he started to think it could be a classic diamond in the rough. It’s a bold, brash thing to say, but Garabedian told me a few weeks ago that the AVI of today reminds him of the 1990s version of Foster City, CA-based Gilead Sciences (NASDAQ: GILD) when it was worth about $500 million, long before it went on to become the world’s largest maker of HIV drugs, worth $32 billion today. Garabedian spent most of eight years in various roles at Gilead during its boom years, before joining another biotech success story in Celgene. Now he says it’s time to apply what he learned in those places.

“Those are experiences at Gilead and Celgene that shaped me, and helped me know what it takes to grow a breakout biotech,” Garabedian says. “I always felt that if I saw another opportunity to do that at another company, that’s something I could be excited about.”

Chris Garabedian

AVI, he says, is the place. There’s certainly room to grow. The stock closed yesterday at $1.55 a share, and the company has a little more than 110 employees, and a market valuation of about $210 million.

“We could make this a breakout biotech. It will take some time. It’s not going to happen in a year,” Garabedian says. “But I think this could be a company valued in the multi-billions in the next several years.”

Before diving into Garabedian’s blueprint for how he intends to lead AVI to that lofty perch, I wanted to know a little more about him. Unlike a lot of biotech CEOs, he never went on to get an MD, a PhD, or an MBA degree. He got a bachelor’s degree from the University of Maryland in marketing, and worked his way up in biotech through various marketing-related roles.

He did some consulting in his first real job out of college for a couple years. He says he “got the biotech itch” while consulting in the early ’90s. He caught on full time with Abbott Laboratories, where he worked on marketing, brand management, and product development in various parts of Abbott’s business in cardiovascular medicine and neurology, he says. “I started to learn how to work with R&D teams,” on things like when to hit the brakes on a new drug development program, when to press on the gas, and what it takes to get the ultimate prize—FDA approval to sell your new drug.

Garabedian’s first experience in a small, nimble biotech came in 1997 as a senior director of marketing for Gilead. He was brought in initially to help craft … Next Page »

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Bothell, WA-based Marina Biotech (NASDAQ: MRNA), the developer of RNA interference treatments, said today it has raised gross proceeds of $6.9 million through a stock offering. The company sold 22.3 million securities units, made up of one share of common stock and one warrant to buy a share of common stock. Marina has said it plans to use the money to support clinical development of its drug for familial adenomatous polyposis. Roth Capital Partners managed the offering. Marina has said it had about $2.3 million in cash on hand at the end of March.

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