Ann Arbor, MI-based RetroSense Therapeutics recently inked a deal with Wayne State University to license a novel gene-therapy approach to treating blindness that was originally studied in the university’s School of Medicine. The treatment offers promise to people suffering with incurable blindness caused by age-related macular degeneration (AMD) and retinitis pigmentosa (RP).

AMD is the leading cause of blindness in people older than 60, affecting more than 8 million people in the United States alone. RP is a genetically-determined eye disease. An estimated 100,000 people in the U.S. have RP, which typically manifests as night blindness and progresses to tunnel vision or complete blindness.

Developed by Zua-Hua Pan, professor of anatomy and cell biology, the technology is designed to convert light-insensitive inner retinal neurons into photosensitive cells. Using a virus that delivers a photoreceptor gene from green algae called channelrhodopsin-2 (ChR2), Pan found that ChR2 made the inner retinal neurons become light sensitive, and that it persisted for long periods in the neurons, ultimately leading to restored responses to light in the visual cortex of the brain.

RetroSense has licensed the technology from Wayne State with the intention of eventually testing the technology in humans. Phase I clinical trials could begin as early as 2013.

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Several San Diego life sciences companies raised money in the past few weeks, based on Form D notifications that companies are required to file with government regulators within 15 days after the first sale of securities in such offerings. The filings do not list the investors, however. Here’s a quick rundown of what I found:

—San Diego-based Biomatrica, which has developed technology that “shrink wraps” biological samples to protect them from degradation, has raised slightly more than $3 million, according to a recent regulatory filing. The company, which Luke profiled in 2009, plans to raise a total $3.3 million in equity and rights. Dow Jones VentureWire reports the company previously raised $1.2 million toward a $5 million equity round, with another $298,000 in rights and securities. The company’s past investors include In-Q-Tel, Mesa Verde Venture Partners, and existing angel investors.

—Celladon, a San Diego startup developing gene therapy treatments for heart attacks and other serious cardiovascular events, has landed $250,000 in debt and securities, according to a recent regulatory filing. The company, which raised $400,000 in July, has received close to $60 million from investors that include Enterprise Partners Venture Capital, Domain Associates, Johnson & Johnson Development Corp., Kleiner Perkins Caufield & Byers, and Venrock. Luke reported last year that a high dose of Celladon’s gene therapy offered a 50 percent lower risk of heart failure when compared with a placebo.

—San Diego’s Abrexa Pharmaceuticals raised $500,000 in a combination of debt, rights, and equity, according to a regulatory filing. Domain Associates’ partner Eckhard Weber is identified as both an executive and director of the startup, but Weber did not respond yesterday to an e-mail query about the company. It also is not listed as a portfolio company on Domain’s website.

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There’s been a deluge of venture capital news over the past week, and a flash flood of VC cash during the second quarter went mostly to San Diego’s life sciences sector. Our briefing begins now.

—San Diego venture firms invested a total of $198.2 million in 29 local startups during the second quarter that ended June 30, according to a breakout of regional data from the MoneyTree Report. The single biggest deal was the $50.4 million for San Diego’s Sangart, but in fact, 24 of the 25 deals were categorized as life sciences deals, accounting for roughly $193.1 million—or more than 97 percent of the $198.2 million total invested here.

—San Diego’s Zogenix (NASDAQ: ZGNX) said it signed an agreement with Durect (NASDAQ: DRRX) of Cupertino, CA, to develop Durect’s long-lasting reformulation of the anti-psychotic drug risperidone (Risperdal) for use with the Zogenix needle-free injector. Zogenix says its collaboration with Durect is a good example of its unfolding strategy, and could lead to the first long-lasting formulation of the anti-psychotic drug available in a needle-free injector for once-a-month use.

—Intellikine, a San Diego startup developing new anti-cancer drugs, hired former Celgene vice president Greg Berk as chief medical officer responsible for overseeing Intellikine’s clinical trials. Intellikine CEO Troy Wilson says he’s encouraged by the company’s progress in developing INK128, a compound that blocks a mutated kinase linked to a variety of cancers from wreaking its havoc in what he calls the PI3K/mTOR signaling pathway.

—In his BioBeat column this week, Luke makes his case for resisting the pressure for life sciences companies to rush into mergers and acquisition deals with Big Pharma. He argues that … Next Page »

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On June 8, Neurologix (NASDAQ: NRGX) released positive data from a trial of its experimental gene therapy treatment in patients with Parkinson’s Disease. It was the latest in a string of impressive announcements from the Fort Lee, NJ-based company, which has been on a roll since March, when the journal Lancet Neurology published six-month results from the study, a Phase 2 clinical trial involving 45 patients.

Has Wall Street applauded? Not exactly. Neurologix, a perennial penny stock, hasn’t traded over a buck since last December—the June 8 announcement bumped its stock from $0.67 to $0.70 a share. (It’s now at $0.79.) But with its Phase 2 completed, the company needs to raise about $50 million to complete the pivotal Phase 3 study that will be necessary to win FDA approval. It won’t be easy, admits Neurologix co-founder Michael Kaplitt, an associate professor of neurological surgery at Weill Cornell Medical College in New York. “The biggest concern” among investors, he says, “is fear of the unknown.”

Such are the frustrations of being a biotech company that’s trying to pioneer an entirely new approach to treating neurological diseases—and one that involves gene therapy, no less. The basic idea of gene therapy is to correct a dysfunctional disease-causing gene by replacing it with a functional gene that’s inserted into the body. It was once a hot concept in biotech, and a technique that many scientists believed could treat a range of diseases.

Then disaster struck. In 1999, 18-year-old Jesse Gelsinger died after receiving an experimental gene therapy for a rare disease, during a trial being conducted at the University of Pennsylvania. Funding for research into gene therapy around the world became scarce.

But Kaplitt and co-founder Matthew During were undeterred. They formed Neurologix in 1999 around a technique that they believed would ameliorate the risks inherent in earlier gene therapy attempts. One main approach to gene therapy involves packing copies of healthy genes into viruses known as “vectors,” which then transport the genes into cells. Scientists believe Gelsinger’s death was caused by an immune reaction to the vector—not to the gene itself. Neurologix’s brain treatment, which During and Kaplitt first described in a 1994 paper, uses a vector called adeno-associated virus 2, which doesn’t trip an immune reaction in humans.

Kaplitt and During also figured out how to deliver the gene only to the part of the brain that goes bad in Parkinson’s patients. Parkinson’s occurs when there’s an imbalance of two brain chemicals, GABA and glutamate, During explains. That, in turn, causes dopamine-producing cells in the brain to die—resulting in the symptoms characteristic of the disease, including … Next Page »

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This week was full with news of progress from New England drug developers.

—Waltham, MA-based antibody drug maker ImmunoGen (NASDAQ: IMGN) sold 7 million shares of stock at $12 apiece. The company had $115.8 million in cash on hand at the end of March, a quarterly report showed.

—Biogen Idec (NASDAQ: BIIB) of Weston, MA, said it received a positive opinion from the committee of the European Medicines Agency, which could help pave the way sales in Europe of fampridine (Fampyra) as a new treatment for multiple sclerosis. The drug is expected to be cleared in about two months, Biogen said.

—My colleague Luke took a look at Cambridge, MA-based Bluebird Bio, a developer of gene therapies that is getting a lot of attention for its two lead programs. One is a drug focused on beta-thalassemia, a genetic disorder in which patients don’t produce enough hemoglobin; the other is a treatment for the brain disorder childhood cerebral adrenoleukodystrophy.

—Cambridge-based Vertex Pharmaceuticals (NASDAQ: VRTX) nabbed FDA approval to market its drug telaprevir (Incivek) in the U.S. as a treatment for hepatitis C. The protease inhibitor can be used as a first-line treatment or for patients who haven’t responded well enough to other treatments. Earlier this month, the FDA approved a competing treatment from Merck  for the liver-damaging disease, which affects 3 million people in the U.S.

—Radius Health of Cambridge took in $91 million in new financing to help advance pivotal Stage 3 clinical trials of its osteoporosis treatment, and merged with an unlisted shell company (“MAC”), to take on the status of an SEC-reporting company and apply to be listed on a national stock exchange. The deal included $66 million in equity funding for Radius, which is developing a bone-building drug, called BA058, modeled after human parathyroid hormone-related protein.

—Casenet, a Bedford, MA-based healthcare software maker, added $3.3 million in equity funding and increased the size of its current financing round to a targeted $15.8 million.

—Cambridge-based drug developer Proteostasis inked a strategic alliance with Ireland-based Elan Pharmaceuticals to develop treatments for neurodegenerative diseases like Parkinson’s, Huntington’s, and multiple sclerosis. Elan gave $20 million initially and could put another $30 million into Proteostasis over the next five years. in return for a 24 percent stake in Proteostais, a seat on its board of directors and scientific advisory board, and the first chance to exclusively license new drug compounds from the collaboration.

—Xconomy New York editor Arlene Weintraub talked to  Cambridge-based Alnylam Pharmaceuticals (NASDAQ: ALNY) CEO John Maraganore, who said the company’s drug for treating liver cancer could make a big splash at this year’s American Society of Clinical Oncology (ASCO) conference on June 4. The company has more safety data on the drug than it did last year, with one of the patients in the trial having been on the drug for a year.

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[Correction: 10:22 am 5/24/11] Bluebird Bio is one of those fortunate companies that can say the top peer-reviewed journals in biomedical research—Science and Nature—have run articles featuring its two lead drug candidates while they are still at the earliest phase of development.

CEO Nick Leschly doesn’t want to sound ungrateful—the buzz doesn’t hurt—but he seems like he’s had enough already.

“We can all go crazy, and write publications and talk about it all we want, but let’s enroll more patients and continue to prove it,” Leschly says.

Cambridge, MA-based Bluebird Bio (formerly Genetix Pharmaceuticals) has raised $65 million in the last 14 months to support its programs for gene therapy, so there are some pretty high expectations that it’s going to have to deliver on at some point. I caught up with Leschly for a quick update while he was in Seattle on Friday for the American Society of Gene and Cell Therapy conference. He said he’s focused on pushing hard and fast on things that matter less to the basic scientists and more to the folks who oversee clinical trials at the FDA.

Here are the highlights of the two programs we discussed:

—Beta-Thalassemia. This is a genetic blood disorder that makes people unable to produce enough hemoglobin to carry oxygen through the bloodstream so that they can live active lives. People can be cured with a bone marrow transplant today, but not all patients are eligible, and there can be dangerous complications with the approach.

The Bluebird treatment is designed to circumvent those issues with a different approach. It extracts a patient’s blood-forming adult stem cells and exposes them in the laboratory to the gene therapy. Bluebird uses a genetically engineered lentivirus to deliver a copy of a gene that essentially programs the cells to start producing hemoglobin on their own. Then the properly functioning blood cells get re-infused into the patient.

Nick Leschly

Last September, Nature published an article about how this approach worked for the first patient who enrolled in a clinical trial. The patient, a young man in Paris who goes by the initial PLB, was soon able to produce enough hemoglobin on his own to quit getting blood transfusions that he had depended on since the age of four.

[Corrected, with updated time frame] Three years later, the young man is still living without the need for transfusions, and no adverse events have popped up to dampen the enthusiasm, Leschly says. “No news on him is good news,” he says.

The bigger issue is that since this is gene therapy, and there have been safety concerns with other approaches in the past, doctors and regulators are inclined to tread carefully. So far, … Next Page »

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Word on the street in Seattle last week was that Big Pharma was sniffing around quite a bit at the American Society of Gene & Cell Therapy annual meeting being held downtown. There was a lot more optimism at this confab than in years past, and Richmond, CA-based Sangamo Biosciences was one of the companies capturing some of the buzz.

Sangamo (NASDAQ: SGMO) had 20 different presentations of data, mostly of the early/preliminary kind, at this meeting. Scientists were there to hear more about Sangamo’s proprietary “zinc-finger protein technology,” which is designed to edit specific DNA sequences inside a cell, to, say, turn off a disease activity. Many investors are waiting to see if Sangamo can deliver the goods on this concept later this year when results are due from a trial of an experimental drug of this variety in 170 patients with diabetic neuropathy—a big potential application of the technology. But most of Sangamo’s presentations at the gene therapy meeting in Seattle focused on using its technology in a number of other diseases, like HIV, hemophilia, and retinal neurodegeneration, to name a few.

Most gene therapy approaches, for those who don’t follow the field every day, involve modifying viruses to carry copies of genes into cells where they can replace missing or faulty genes at the root cause of certain diseases. Gene therapy was hyped in the early 1990s as a potential cure-all for all kinds of ailments that have evaded traditional drug-based approaches. Safety concerns have popped up more than once, and there still aren’t any FDA approved gene therapies, although there have been some encouraging results lately that have sparked a bit of a comeback.

“I’ve been coming to this meeting since 1990,” Sangamo CEO Edward Lanphier said during a break at a downtown hotel on Friday. “It goes up and down in terms of what’s hot and what’s not.”

Edward Lanphier

Here’s a couple key programs that Sangamo highlighted at the conference, and which I discussed with Lanphier.

—Sangamo scientist Michael Holmes presented data from a study in mice which showed encouraging results in a specific type of hemophilia. In this case, the disease comes from a deficiency of a protein known as Factor IX. Scientists gave a single injection of one of Sangamo’s zinc-finger compounds and found that mice who got the injection were able to produce Factor IX on their own in high enough levels to achieve normal blood clotting, Lanphier says.

“The efficiency is impressive and resulted in sustained therapeutic levels of Factor IX in the mice,” says Barrie Carter, the president of the ASGCT, and a member of Sangamo’s scientific advisory board.

Mice aren’t the same as human beings, so this program obviously has a long way to go. But if Sangamo can efficiently deliver its zinc-finger drug into human cells, it could have a big impact. A treatment like this may enable patients to quit taking regular injections of Factor IX protein replacement therapy, enabling them to save those drugs for … Next Page »

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For those who have not been watching or involved, gene and cell therapy is experiencing a state of resurgence, driven by a series of positive achievements over the last three to four years. These are exciting times for those who kept the faith over the last two decades and pushed onward. There is buoyancy in the field and a demonstrable interest by large pharma and biotech companies. The enthusiasm about recent advances will be on display this week, May 18-21, at the 14th annual meeting of the American Society of Gene and Cell Therapy at the Seattle Convention Center.

After 15 to 20 years of trials, clinical results are powering a resurgence of enthusiasm, right on the standard biotechnology clinical developmental timelines. Trials in patients, mostly young children, having debilitating inherited immune deficiencies are showing remarkable reconstitution of immune systems. Success rates are at least equivalent to bone marrow transplantation, the only other possible treatment for these diseases. Currently, the gene delivery systems are being modified to decrease the risk of clonal expansion leading to leukemia in some cases that is an undesirable side effect. Several groups tested gene therapy for an inherited eye disease caused by a mutant gene leading to retinal degeneration and blindness. A viral vector placed under the retina gave substantial gains in retinal sensitivity and improvement in visual mobility. These advances in patients with rare, inherited genetic diseases provide proof of concept for gene therapy.

Gene and cell therapies are also directed at complex multigenic and acquired diseases, such as cancer. Thus, oncolytic viruses replicate in cancer cells to destroy them and may induce immune responses against them, to give a double whammy. Oncolytic viruses have progressed into advanced phase II and phase III trials. Of course, over the last year we have seen approval for marketing of the first cell therapy, sipuleucel-T (Provenge), for prostate cancer developed here in Seattle by Dendreon. Other cell therapies, particularly those in which T-cells are specifically modified to enhance their ability to recognized and destroy cancer cells, are making substantial strides. Heart failure is being targeted and a viral vector (AAV) and a non-viral plasmid DNA delivered by interventional catheterization, are advancing in clinical trials. In Parkinson’s disease patients, direct injection into the brain shows evidence for sustained gene expression for up to two years and, in at least one Phase II trial, statistical evidence for improvement.

Development of new technologies such as stem cells, small RNAs and gene-targeting continues apace. Testing of stem cells has now advanced into clinical trials. The ability to modify T-cells or hematopoietic stem cells is being coupled with gene-targeting technology, like zinc finger nucleases. This represents the next step in gene therapy by … Next Page »

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Investors are rewarding Bluebird Bio for wracking up accolades with its experimental gene therapies for serious genetic diseases. The Cambridge, MA-based biotech firm has brought in $30 million in a Series C round of funding, just over year after investors pumped $35 million into the firm in its second-round financing.

ARCH Venture Partners joined the investor syndicate at Bluebird, and Steven Gillis, a managing director at ARCH, took a seat on biotech’s board of directors. The new round also drew investments from previous Bluebird backers Third Rock Ventures, TVM Capital, Forbion Capital Partners, and Easton Capital Investment Group. Nick Leschly, president and CEO of Bluebird, says that the company hadn’t exhausted its cash from its previous financing prior to closing this latest round of funding, but the additional capital will help the firm advance its clinical development plans, as well as invest in its technology.

Bluebird (formerly Genetix Pharmaceuticals) has helped change the headlines about gene therapy, from those of yesteryear that highlighted dangerous side effects, to ones describing renewed promise in the field. In September, the prestigious journal Nature ran an article about how the company’s gene therapy for an inherited blood disorder called beta-thalassemia provided significant benefits for a man in his early 20s with the disease. There are also four patients who have been treated with a version of the firm’s therapy for childhood cerebral adrenoleukodystrophy (CCALD)—a genetic brain disorder also known as “Lorenzo’s Oil” disease. And the firm revealed data in May 2010 that showed its treatment had stabilized CCALD in two patients who had been treated three years earlier.

With its new financing in hand, Bluebird is planning to increase enrollment in an ongoing Phase I/II trial for its beta-thalassemia treatment over the next 12 months to about 10 patients. The treatment might also be effective in treating sickle cell anemia, and the firm plans to test it in people with that disorder too. Toward the end of the year, Leschly says, the firm aims to begin a clinical trial in the U.S. and Europe for a CCALD treatment. The trial would follow the ongoing pilot study in CCALD patients. In the meantime, the company plans to invest further in its core gene therapy technology, which Leschly says could be used to treat a variety of severe genetic diseases.

“The idea here is really to accelerate our … Next Page »

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Cambridge, MA-based Bluebird Bio, a gene therapy company, said today it has signed an agreement with the French Muscular Dystrophy Association (AFM) to develop a treatment for beta-thalassemia (a genetic blood disorder) and sickle cell anemia. The deal is worth $1.4 million upfront, plus as much as $2.8 million in credit to manufacture clinical trial material at Généthon, AFM’s bio-therapy research center. Bluebird, which my colleague Luke profiled last September, uses a genetically engineered lentivirus to deliver a copy of a gene that enables the body to produce hemoglobin, the protein in red blood cells that carries oxygen. The company’s investors include Third Rock Ventures, TVM Capital, Forbion Capital Partners, Easton Capital, and Genzyme Ventures.

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One of our local billionaires made a couple of significant biotech investments this week, while one of the venerable names from the biotech scene faded away.

—The Bill & Melinda Gates Foundation made its first-ever direct equity investment in a for-profit biotech company last week, when it plunked down $10 million on Research Triangle Park, NC-based Liquidia Technologies. As the foundation’s Doug Holtzman explained to me in an exclusive interview, this deal was crafted to provide maximum flexibility so Liquidia can build out its technology for making vaccines against various scourges of the developing world—instead of being hemmed in to carry out work on one specific project. Separately, my Boston colleague Ryan McBride reported on how Gates personally invested in Cambridge, MA-based Nimbus Discovery, which is seeking to use computer models to improve drug discovery.

—Seattle-based Targeted Genetics is no longer Seattle-based Targeted Genetics. The venerable gene therapy company is now based out of London, goes by the new name AmpliPhi Biosciences, and is primarily focused on anti-bacterial drugs. It’s the end of an era for one of the region’s important companies of the 1990s and early 2000s.

—Calypso Medical Technologies looked to be on the cusp of big things when it raised $50 million in venture capital in September 2009, but it was actually going through hard times, as I explained in a feature story this week. The Seattle-based medical device company struggled through a tough couple of years when hospitals were unwilling to spend big bucks for its radiation-pinpointing technology for prostate cancer, although the new CEO says hospitals are feeling more confident about spending now that the federal healthcare reform law has passed and the stock market is up.

—The Seattle-based Institute for Systems Biology struck yet another collaboration this week, this time through a partnership with Covance to study brain tumors. Terms weren’t disclosed.

—About 1,000 people turned out for the big Life Science Innovation Northwest conference last week put together by the Washington Biotechnology & Biomedical Association, making this the biggest local biotech event in years—or maybe ever. I didn’t have any one major scoop from this confab, but I put together a half-dozen mini-scoops of new information on small companies presenting at this year’s conference. Here are a few companies that I paid close attention to—PhaseRx, Cardiac Insight, Acqueduct Neurosciences, and Integrated Diagnostics.

—This week’s edition of the BioBeat column, now a regular Monday feature, focused on the state of dysfunction in the IPO market for new biotech companies.

—Lastly, we had a guest editorial from Stewart Lyman about how biotech companies sometimes seek advice for all the wrong reasons. If you don’t already, this post will make you think twice about whether to be impressed when a company brags about how it has a Nobel Laureate or two on its scientific advisory board.

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Targeted Genetics has been a shell of its former self for a couple years now, but today it’s officially no longer the same old Targeted Genetics.

The Seattle-based company, a one-time trailblazer in the field of gene therapy, said today it has made a slew of changes to its business, including ditching the old name in favor of a new one—AmpliPhi Biosciences (pronounced like the thing that cranks up the sound coming from a guitar).

The re-invented company, traded on the Pink Sheets, is now headquartered out of London, the home of new CEO Edward Cappabianca. AmpliPhi is the creation of the merger of Targeted Genetics and London-based Biocontrol—although the emphasis in today’s release is focused on what Biocontrol brought to the table. The new company is going to focus on bacteriophage therapies, designed to fight stubborn antibiotic-resistant bugs like Pseudomonas aeruginosa. AmpliPhi says it has nailed down research grants for part of its drug development programs, including support from the Cystic Fibrosis Foundation of America.

The new entity is still holding onto some old Targeted Genetics intellectual property, and it stands to collect royalties if any partners like Amsterdam Molecular Therapeutics, San Diego-based Celladon and Cambridge, MA-based Genzyme (NASDAQ: GENZ) are able to create new drugs that use Targeted’s techniques for delivering specific gene therapies where they need to go in cells.

Targeted Genetics had been struggling to stay afloat for two years now, as it ran out of cash and was unable to keep raising more as investors lost interest in the once highflying field of gene therapy in the 1990s. It burned through more than $315 million in investor capital during its 19-year history, leaving many investors with holdings that were basically worthless. The company did, however, leave a profound mark on the Seattle biotech community as a training ground for a generation of scientific and managerial talent. Founder and longtime CEO H. Stewart Parker recently landed a new gig as the CEO of the Infectious Disease Research Institute, bringing her business experience to the prolific global health nonprofit organization.

I’ve personally covered Targeted Genetics for almost 10 years now, and seen it experience a few highs, like the time its gene therapy showed an effect against a congenital form of blindness. There were also plenty of lows, like the time a clinical trial showed its most advanced gene therapy failed to help patients with cystic fibrosis, and when a patient died in a rheumatoid arthritis trial, raising suspicion that Targeted’s therapy was responsible (ultimately, it wasn’t).

AmpliPhi Biosciences will retain a Seattle office focusing on finance, business development, investor relations, and capitalizing on the remaining gene therapy assets, says David Poston, the longtime finance chief for Targeted Genetics. Former CEO Susan Robinson “is pursuing other Seattle-based biotech projects, which may include forming her own company,” Poston says. The new company strategy, he says, amount to “exciting times, indeed.”

We don’t have a London bureau so this will probably be my last post about the company now known as AmpliPhi.

Targeted, R.I.P.

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[Updated: 2:15 pm] H. Stewart Parker did some soul-searching after her dreams fizzled out at Seattle-based Targeted Genetics, but now the well-known biotech executive has found herself a big new challenge at the Infectious Disease Research Institute.

Parker, 55, the founder and longtime CEO of Targeted Genetics, has agreed to sign on as the CEO of IDRI, the nonprofit global health research center on Seattle’s First Hill. She starts on March 1.

IDRI is pretty much invisible in its hometown, but it is well-known in global health circles as a bustling center for R&D. The nonprofit, founded by immunologist Steve Reed in 1993, now has 94 employees, and an annual budget of about $25 million—half of which comes from the Bill & Melinda Gates Foundation, according to president Curt Malloy. The institute has seen about five-fold growth in the past six years, adding capabilities for vaccine research and development, low-cost diagnostics, and early-stage drug discovery—particularly a tuberculosis treatment program supported by Eli Lilly.

Reed will remain the head of R&D at IDRI, while he continues in his other work as CEO of Seattle-based Immune Design, a vaccine spinoff from IDRI and Caltech that has raised more than $50 million in venture capital. By adding Parker, IDRI is getting its first full-time CEO in the two years that have passed since interim CEO Steve Davis stepped down. Parker, with her experience at Targeted Genetics, knows all about the perils of taking promising science through the clinical development process, and all the money and collaborations it takes to support that enterprise.

“We really pride ourselves on how well we work with the for-profit sector, and she will bring a lot of experience in that area,” Malloy says. “She has product development focus, and operational expertise.” When I asked if Parker will help IDRI raise its public profile, and help improve community fundraising, Malloy didn’t answer directly, but it sounded like a yes. “We’ve kept our heads down too long, we really are a story that hasn’t been told,” Malloy says.

[Updated comment from Parker] “IDRI is the best kept secret in town,” Parker says. “This felt like a natural fit for me. I can’t wait.”

The fit was good, Parker says, because IDRI has an entrepreneurial spirit and an understanding of how things work in industry, which is rare in a nonprofit. Reed, who she has known for years since he was a co-founder of Seattle-based Corixa, personally called her to talk about the position almost a year ago, Parker says. She says she envisions working as a “co-captain” in which Reed continues to drive the R&D effort, while she focuses on key business functions like business development, strategy, fundraising, and “creating the opportunity for our scientists to excel,” she says. She adds: “Our skills are complementary.”

Since she left Targeted Genetics in November 2008, Parker took some time off to think about her next move, as I discussed in this December 2009 feature. She eventually took a part-time role with the Washington Biotechnology & Biomedical Association as a mentor for budding biotech entrepreneurs. It was a role she had unusual qualifications for, as one of the first employees at Immunex in 1981, and as the head of Targeted Genetics from the time it spun off from Immunex in 1992. Parker says she plans to step down from the WBBA role after a transition period.

Like any job, this will involve a learning curve, but it has a new wrinkle for Parker. Her past two jobs were basically with companies that were just getting started, where the culture was being created. IDRI is different in that it has an established culture which Parker will learn. This will be a little like some of her past experience as a board member, in which she has had to get up to speed on established organizations.

“I’m a good listener, I believe in teamwork, I think it will be OK,” she says.

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Seattle’s hot biotech company of the moment survived an unusual public hearing this week that could have put a serious crimp in its ability to sell its drug.

—Seattle-based Dendreon (NASDAQ: DNDN) dodged a bullet at a public hearing this week held by the Centers for Medicare and Medicaid Services. The government-run health insurance plan for the poor and people 65 and older convened a panel of physicians and researchers to weigh the evidence for Dendreon’s sipuleucel-T (Provenge). The panel expressed an intermediate degree of confidence that the drug does prolong lives of men with prostate cancer when used according to its FDA-approved label, although the panel disapproved of use for unapproved “off-label” uses.

—Swiss pharmaceutical giant Roche made big news this week when it announced a global R&D restructuring program, and specifically said it plans to terminate its efforts to discover and develop RNA interference drugs. This was a surprise given that Roche is the world’s biggest spender on pharma R&D, and a prominent benefactor of two leaders in this emerging field of therapy—Cambridge, MA-based Alnylam Pharmaceuticals (NASDAQ: ALNY) and Vancouver, BC-based Tekmira Pharmaceuticals (NASDAQ: TKMR). Alnylam stock fell 5 percent on the news, while Tekmira dropped almost 14 percent.

—Allozyne, the Seattle-based developer of new techniques to engineer protein drugs, said this week that its second drug candidate for autoimmune diseases has passed a couple important animal tests and is being primed for clinical trials. This treatment, a “bispecific” antibody designed to hit two targets on inflammatory cells instead of just one, is starting to generate just as much interest among Big Pharma partners as Allozyne’s lead candidate for multiple sclerosis, which has already completed a clinical trial, CEO Meenu Chhabra said in this Xconomy exclusive.

—Arch Venture Partners, the largest life sciences venture investor in Washington state, came close, but wasn’t able to grab the proverbial cigar last week through an IPO of Ikaria. Arch was in line to see its early investment in Ikaria transformed into liquid holdings worth more than $50 million, until, at the last moment, the company withdrew its IPO when it didn’t find the kind of investor demand it wanted to see. Arch’s Bob Nelsen acknowledged he was disappointed, in an exclusive interview with Xconomy, but said Ikaria will still go on as one of those rare birds in biotech—a profitable company.

—Since I like to mix things up around here, I took some time to learn about what Redmond, WA-based Physio-Control is doing to generate some interest among docs attending this week’s American Heart Association meeting in Chicago. The company, part of medical device giant Medtronic, rolled out the latest iteration of its vision for smooth wireless transmission of heart data from ambulances to the hospital. Part of this plan involves a partnership with a hot health IT company, San Antonio, TX-based AirStrip Technologies, which makes a high-resolution iPhone app that cardiologists can use to examine a patient’s vitals.

—Todd Patrick, one of the more successful life sciences entrepreneurs of the past decade in the Northwest, has taken a new gig as the CEO of Los Angeles-based C3 Jian.

—Another well-known CEO around town, Ron Berenson, made his exit from HemaQuest Pharmaceuticals, as he is being replaced by John Longenecker.

—And lastly, Seattle-based gene therapy pioneer Targeted Genetics, which has been gradually fading away over the past couple years, said this week it is seeking to merge with London-based Biocontrol. Shareholders at Biocontrol are being asked to OK this deal.

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Targeted Genetics, the Seattle-based gene therapy company that has struggled to survive the past two years, said today it has agreed to merge with London-based Biocontrol. The deal seeks to combine Biocontrol’s science with Targeted Genetics’ technology for using adeno-associated viruses to deliver gene therapies inside cells. The deal must be approved by Biocontrol shareholders.

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Ceregene, the San Diego-based gene therapy company, said today it has raised $11.5 million in a Series D venture round. Hamilton BioVentures and Alta Partners led the deal, which included MPM Capital and Investor Growth Capital. Ceregene said plans to use the money to complete a Phase 2b clinical trial of its experimental treatment CERE-120 for Parkinson’s disease. Back in December 2008, Ceregene said a mid-stage trial of 58 patients failed to show a statistically significant advantage when compared to a placebo. For more on Ceregene and its strategy against Parkinson’s disease, check out this profile we ran back in October 2008.

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Quite a few biotech entrepreneurs would be happy to trade places with Sangamo Biosciences founder and CEO Ed Lanphier. His company has a hammerlock on the intellectual property for a leading-edge genetic technology that a lot of academic scientists love to write about in top peer-reviewed journals like Nature. Big partners like Dow Chemical and Sigma-Aldrich are shelling out cash to get licenses.

And while Richmond, CA-based Sangamo hasn’t yet proven that it can turn this technology into the basis for a drug company, it is about a year or so away from finding out if it has created a first-of-its-kind treatment for a common complication of diabetes, one of the biggest markets in the pharmaceutical business.

So what do investors think of all this? The stock chart (NASDAQ: SGMO) tells a pretty grim story. Sangamo has been on a steady downhill slide, falling from a 52-week high of $7.45 to $3.92 at last week’s close.

Lanphier, who founded the company 15 years ago, shrugs.

“There are things I know something about, and things I know little about. The stock market is one of the latter,” Lanphier says.

Of course, Lanphier does have some ideas about what’s going on. Many of the general-interest, diversified fund managers on Wall Street just don’t have the same appetite for biotechnology that they did when the Human Genome Project was all over the news. Even the mainstay biotech funds, with PhDs on staff comfortable with researching a company like Sangamo, have turned cautious in the downturn, placing safer bets on drugs and technologies that have already passed their critical experiments. Other companies with reputations for innovative science, like South San Francisco-based Exelixis (NASDAQ: EXEL), have also seen investors’ patience run thin.

Ed Lanphier

So what does Sangamo have that’s interesting, yet hard to pin down with a quantitative value? It’s called zinc finger protein (ZFP) technology. The goal at the company, founded 15 years ago with science from MIT, Johns Hopkins University, Johnson & Johnson, is to develop biologic molecules that can specifically turn on, or turn off, certain genes through a biological mechanism that’s found in everything from yeast to worms to mice to human beings. This technology … Next Page »

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The third quarter of 2010 is going out with a monsoon in New England. It seems like a good time to hole up indoors and look back at some of the top stories we’ve done at Xconomy Boston over the past three months.

These are our editors’ picks. They aren’t necessarily the ones that got the most traffic or the most attention. Rather, they are stories that highlight our unique style of on-the-scene reporting and in-depth analysis, and will stand the test of time. They range from startup profiles in health IT, security software, and drug development, to analysis pieces on leading companies’ acquisition and expansion strategies, to unique venture capital perspectives and quirky, strange-but-true facts about New England innovation leaders.

So, without further ado, here are our top 20 stories of the third quarter, in reverse chronological order (plus a bonus story, in honor of Unica founder Yuchun Lee, a former member of the MIT Blackjack Team, selling his company to IBM for $21 a share):

Genzyme Boss Henri Termeer Not Ready to Sell to Sanofi, Ride Into the Sunset, Sources Say

MeYou Health Enters Social Gaming Realm with Daily Challenge for Improving Well-Being

IBM’s Software Acquisition Strategy in Massachusetts (Plus Tips on Getting Acquired) From VP Mike Loria

Skyhook, Fighting for Its Life in Suit Against Google, Cries Foul: “Call in the Referees and Review the Tape”

Bluebird Bio, Third Rock & Genzyme’s Gene Therapy Bet, Shows Promise for Blood Disorder

Who Knew? Part 3: Xconomy Uncovers Even More Strange-But-True Facts About Boston’s Innovation Leaders

PerkinElmer Expects to Make Acquisitions After $500M Business Sale: CEO Talks Boston-Area Talent and Growth in Software, Imaging

A123 Opens Lithium Ion Battery Plant in Michigan, Wants to Create Global Hub for Electric Vehicles

Good Start Genetics Emerges from Stealth with $18M Series A Round

Reality Show Project Seeks to Capture MassChallenge Competitors in Their Entrepreneurial Element

Vertex Nails Third Big Trial With Hepatitis C Drug, In Toughest Patients to Treat … Next Page »

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Genzyme and Third Rock Ventures bet $35 million six months ago on a Cambridge, MA-based gene therapy company. Despite all the ups and downs with gene therapy over the years, now we can see why they placed the bet.

The newly renamed Bluebird Bio, formerly known as Genetix Pharmaceuticals, is coming out today with an eye-opening paper in Nature. The study says Bluebird’s experimental gene therapy offered a startling benefit for the first patient enrolled in a clinical trial, designed to treat a genetic blood disorder called beta-thalassemia. The patient, in his early 20s, had been forced to live with monthly blood transfusions since the age of four, because the thalassemia made it impossible for him to produce enough hemoglobin to carry adequate oxygen through the blood.

Since getting a single shot of the gene therapy 27 months ago, the young man has been able to produce enough hemoglobin on his own to quit getting blood transfusions. That has made it possible for him to feel vigorous enough to hold down a full-time job as a cook in Paris, said Bluebird CEO Nick Leschly. An estimated 60,000 people around the world suffer from thalassemia.

“For the first time, a patient with severe beta-thalassemia is living without the need for transfusions over a sustained period of time,” said one of the study’s co-authors, Marina Cavazzana-Calvo, a professor of hematology at the University of Paris, in a statement. Leschly hasn’t spoken to the patient, but added: “The treating physician who has talked to him has said his life has been transformed.”

Gene therapy has been one of the most glamorous, and some would say overhyped fields of biotech of the past two decades. The idea is to alter viruses that carry copies of genes into cells, where they can replace missing or faulty genes at the root of certain types of disease. This technique rode a wave of scientific enthusiasm in the early 1990s, leading to the formation of more than 100 biotech companies, and to a nearly two-decade long research effort at Genzyme. Some promising anecdotal stories have emerged over the years, but there have also been some high-profile safety concerns and clinical failures. There are still no FDA-approved gene therapies on the U.S. market.

Nick Leschly

But Genzyme and Third Rock made their $35 million investment back in March based on renewed optimism. Bluebird, which has been around since the early ’90s, is planning its next moves around the treatment of beta-thalassemia and a debilitating brain disorder called adrenoleukodystrophy.

Of course, one patient in a clinical trial is only one patient, and it’s nowhere near the kind of convincing evidence that Bluebird will need to win market clearance from regulators and broad market acceptance from doctors and patients. But it’s the sort of data that will prompt Bluebird to recruit about another 10 patients to see if the experience can be replicated, setting the stage for more rigorous testing, Leschly says.

For now, scientists will dig into the details and wonder about why this might be working. The Bluebird treatment uses a genetically engineered lentivirus to deliver a copy of a gene that enables the body to produce hemoglobin, the protein that carries oxygen in red blood cells throughout the body. While many gene therapies of the past have struggled … Next Page »

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There’s a changing of the guard happening over at one of the historic addresses in Seattle biotech—1100 Olive Way. This former car dealership, which for more than 15 years was home to Targeted Genetics’ leading-edge gene therapy work, is now going to be the center of a new initiative in pediatric cancer studies at Seattle Children’s Research Institute.

This story jumped out at me literally, as I noticed a brand new paint job and set of Children’s logos plastered on the door, just off the corner of Olive Way and Boren Avenue. (For all of you who wonder where I get my story ideas, this one came from the seat of my bicycle as I pedaled by yesterday morning on my way to the office.)

It turns out that Children’s, which already occupies a state-of-the-art research building at 9th and Stewart just a few blocks away, is spiffing up the former Targeted Genetics facility to turn it into a pediatric cancer research center led by Michael Jensen, a newly recruited scientist from City of Hope in Duarte, CA. Jensen will lead a team there that studies immunotherapy techniques, in which scientists seek to stimulate the body’s own immune system to fight cancer cells as a foreign invader like a virus or bacteria. The old facility, which used to house Targeted Genetics’ gene therapy manufacturing plant, will eventually house new labs. It will also become home for a “T-cell re-engineering and production factory” in which T-cells of the immune system are harvested from the blood and re-programmed to fight cancer, says Teri Thomas, a spokeswoman for Seattle Children’s.

Targeted Genetics, meanwhile, has shrunk down to just four employees and some part-time consultants, with a headquarters downtown at 601 Union Street, the Two Union Square building. The company terminated its lease on the old 1100 Olive Way facility in November, and then consolidated some offices in the neighboring Metropolitan Park West building until the end of July, when it moved its remaining employees to the downtown building.

The 1100 Olive building has a lot of sentimental value to an entire generation of Seattle biotech talent, who learned the industry ropes there under longtime CEO H. Stewart Parker. Targeted Genetics has had well-documented financial struggles the past couple years. It received a critical lifeline last September when Cambridge, MA-based Genzyme (NASDAQ: GENZ) agreed to acquire some of its most valuable intellectual property, used for manufacturing certain viruses for gene therapy experiments, for $7 million.

With no need for its own manufacturing space anymore, Targeted Genetics has been able to downsize further. The company still has a couple of proprietary drug development programs—one for a rare eye disorder called Leber’s congenital amaurosis, and another for Huntington’s disease. The clinical trials for those gene therapy programs are being run elsewhere, at University College London and the University of Iowa, respectively. Another program that Targeted Genetics is watching very closely, and which could generate some milestone payments, is a heart failure treatment in development by San Diego-based Celladon.

Targeted Genetics’ last statement about its financial health came out on June 1, and CEO Susan Robinson told me in a phone call yesterday that she wasn’t going to offer any further update. The company said in that statement it had $5.1 million in cash and investments left on Dec. 31, 2009. In that release, Robinson said she was evaluating options, like selling the company, or liquidating assets while sending future royalty streams to shareholders. Much of the value of that royalty stream will depend on what happens to Celladon’s heart failure program, which yielded some promising results at a medical meeting in May.

Even if that program advances with the key modified viral delivery vector from Targeted Genetics to help heart failure patients, the manufacturing will be done somewhere else. And it’s possible that a new generation of immune-based treatment for kids with cancer will emerge from 1100 Olive Way. It may not be much consolation for Targeted Genetics employees who lost their jobs or shareholders who lost their money, but Robinson saw something positive about that for the Seattle biotech community.

“I’m glad to see that the building is now being occupied by an institution in Seattle that will use it for what it’s been used for the past 15 years, and that’s research and development,” says Robinson.

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