Drug development programs got extended at two San Diego life sciences companies, while others had some good news on the fund-raising front. We wrap it all up for you here.

—Fate Therapeutics, a startup working to supply “industrialized” stem cells for the pharmaceutical industry without using embryos, said it raised $30 million in venture capital. That brings the total amount raised by the San Diego-based company to about $50 million since its inception two years ago.

—Cadence Pharmaceuticals (NASDAQ: CADX) said the FDA has delayed its review of the San Diego company’s intravenous pain reliever by three months, to Feb. 12. Cadence provided additional data to the FDA after an advisory panel raised concerns about liver damage from excessive doses of acetaminophen. But Cadence said it remains confident it will win FDA approval of its drug, which contains acetaminophen.

—Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) and its Big Pharma partner, Genzyme (NASDAQ: GENZ), have extended the timeline for their much-anticipated cholesterol-lowering drug by nearly a year. The companies reported encouraging results from a clinical trial, but noted that four out of 34 patients saw their liver enzymes increase to three times normal, a sign of potential liver damage. The companies plan to tinker with the dose of the injectible drug in future trials.

—San Diego-based NextImage Medical, a developer of a Web-based system for scheduling and managing diagnostic imaging services, reporting raising $5 million in a venture round led by Chrysalis Ventures of Louisville, KY.

—San Diego-based Altair Therapeutics, a company developing inhalable drugs to block inflammatory proteins involved in asthma and other respiratory diseases, has closed on the second part of a Series A venture financing, bringing the total amount raises this year to $17 million.

—San Diego-based Cyntellect, which makes work stations used by biotechs for cell analysis, purification, and processing, raised $15.5 million so far in a secondary round that aims to raise a total of $18.6 million, according to a recent regulatory filing.

—GenVault, a Carlsbad, CA-based company that markets dry-storage technologies that allow scientists to store biological samples at room temperature, said it expects to break even by the end of next year. The startup has raised about $32 million so far.

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Several of New England’s life sciences firms had good news to report this week.

—Ryan gave a run-down of the key insights to emerge from our Xconomy Forum on pharma innovation. Sirtris CEO Christoph Westphal, for example, offered insight into one of the biggest biological mysteries around the Xconomy office: how Luke manages to eat so much and stay so thin.

—Cambridge, MA-based Gloucester Pharmaceuticals won FDA approval for romidepsin (Istodax), a treatment for a rare cancer called cutaneous T-cell lymphoma. Gloucester expects to begin marketing the drug in January.

—Noah Beerman took the reins of RXi Pharmaceuticals (NASDAQ: RXII), a developer of RNA interference drugs. Previous president and CEO Tod Woolf will remain on the Worcester, MA-based company’s scientific advisory board.

—Lexington, MA-based Concert Pharmaceuticals started human testing of an anti-HIV drug called CTP-518. Reaching the milestone will trigger a $12 million payment from Concert’s partner, GlaxoSmithKline.

—After announcing earlier this year that it was considering strategic options, including a sale, Cambridge-based Helicos Biosciences (NASDAQ: HLCS) took itself off the block, citing “improving standalone prospects and its current market valuation.”

—Cambridge-based Ironwood Pharmaceuticals inked a $75 million-plus deal with Japan-based Astellas Pharma. The agreement gives Astellas rights to market Ironwood’s lead drug candidate, the constipation treatment linaclotide, in Japan, Indonesia, the Philippines, Korea, Taiwan, and Thailand.

—Aileron Therapeutics, also of Cambridge, published research in the journal Nature indicating that its “stapled peptide” technology can be used to block the production of a protein called Notch that’s implicated in uncontrolled growth of cancer cells. Luke put the news in the context of Aileron’s efforts to develop drugs that hit previously unreachable targets.

—Ryan checked in with Cambridge-based electronic health records provider Dossia. After launching to much fanfare in December 2006, the non-profit is making slow progress in getting its system adopted, but it has recently solidified its leadership team and made other changes it hopes will help.

—Cambridge-based Alnylam Pharmaceuticals (NASDAQ:ALNY) announced the formation of an internal group called Alnylam Biotherapeutics focused on applying the company’s RNAi technology to increase the output of biomanufacturing processes.

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Some San Diego life sciences companies reported a burst of new financing, while embattled Sequenom told investors it’s trying to conserve its available cash. Here’s our rundown of the latest highlights:

—San Diego’s Trius Therapeutics, a venture-backed biotech developing a new antibiotic for treating acute and life-threatening bacterial infections, disclosed plans to raise as much as $86 million in an initial public stock offering. With additional funding, the company will proceed to Phase 3 clinical trials of torezolid, which Trius describes as a second-generation successor to linezolid, the Pfizer antibiotic known as Zyvox.

—Life Technologies (NASDAQ: [[ticker: LIFE]]), the Carlsbad, CA-based provider of biotech instruments and lab supplies, agreed to acquire Woburn, MA-based BioTrove, which has developed a high throughput gene expression and genotyping analysis system.

— SpectraScience, the San Diego medical device maker, has raised more than $4.3 million through a private placement that combines preferred shares and warrants. SpectraScience (OTCBB: [[ticker: SCIE]]) CEO Jim Hitchin told Bruce the offering closes a $5 million round the company began earlier this year.

—PaxVax, a San Diego startup backed by Seattle’s Ignition Capital, has raised $2 million of a planned $6 million investment round. The biotech founded in early 2007 is developing a new type of vaccine that is administered as oral tablets and avoids much of the requirements that conventional vaccines require.

—Sequenom, San Diego’s embattled diagnostics company, said it expects to end the year with $39 million in cash—but that’s not enough to get through 2010 without raising funds or slowing spending. In April, Sequenom (NASDAQ: [[ticker: SQNM]]) disclosed that it had “mishandled data” from a prenatal Down syndrome diagnostic test, indefinitely postponing that product launch.

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Several of New England’s tech and life sciences firms got juicy deals the past week and a half.

—Boston’s RunMyErrand, an online clearinghouse where busy people can find helpers for odd jobs, raised $1 million in a Series A venture financing round. The cash, from California investors Baseline Ventures and Maples Investments, will help the startup staff up and expand to San Francisco.

—Cambridge, MA-based Cequent Pharmaceuticals raised $3.35 million in the first tranche of its second venture financing round; the round could eventually total $15 million. Cequent, a developer of RNA-interference based drugs, raised $15 million in its 2007 Series A round from Ampersand Ventures, Pappas Ventures, Yasuda, and Novartis Option Fund.

—Pulmatrix raised $30.2 million in a Series B venture round led by Arch Venture Partners and Novartis Bioventures Fund and joined by Polaris Venture Partners and 5AM Ventures. The Lexington, MA-based startup is developing drugs that prevent a variety of microbes, including influenza, from infecting the lungs.

—GTC Biotherapeutics (NASDAQ:GTCB) of Framingham, MA, raised $10 million in a sale of stock to French biotech drug maker LFB Biotechnologies, already a major shareholder

—Waltham, MA-based On-Q-ity, a developer of cancer diagnostic tools, reportedly raised $21 million in a Series A round of venture capital from Mohr Davidow Ventures, Bessemer Venture Partners, Physic Ventures, and Northgate Capital. The startup was formed through the merger of two Mohr Davidow portfolio companies, CELLective Diagnostics and The DNA Repair Company.

—Boston’s Flybridge Capital Partners helped funnel $3.4 million into New York-based open-source database developer 10gen. Returning investor Union Square Ventures also contributed to the Series B round.

—Special effects software startup GenArts of Cambridge, MA, acquired St. Louis, MO-based Wondertouch, whose software generates so-called “particle-based” special effects. Financial terms of the deal were not disclosed. Wade took a fun look at the companies’ technologies.

—We got the inside scoop last week at our Xconomy event on pharmaceutical innovation when Boston-based Enlight Biosciences revealed that it struck a deal with Abbott Laboratories (NYSE:ABT). Abbott agreed to join the consortium of big pharmas that are …Next Page »

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Sanofi-Aventis (NYSE: SNY) hosted a large event at its R&D site in Cambridge, MA, yesterday to make its pitch for why Boston-area biotech companies should want to form partnerships with the French drug giant. It was an impressive show of force by the company, which has historically kept a lower profile in local biotech circles than some of its Big Pharma competitors.

The top brass from Sanofi were there at the firm’s Cambridge Research Center in Kendall Square. Sanofi CEO Chris Viehbacher outlined the global drug-maker’s plans to form stronger ties with biotech firms in Boston and around the world as part of a broader strategy to build a more sustainable business. Viehbacher also confirmed that Sanofi plans to form a venture capital unit to invest in biotech companies and further efforts to access innovation from outside of the company.

Sanofi, like many other Big Pharma companies, is looking outside of its organization to biotech firms for what Viehbacher called the “right brain activity” that leads to creativity and innovation. Sanofi’s shift toward more external product development efforts includes a partnership deal with Merrimack Pharmaceuticals, announced last month, focused on the Cambridge, MA-based biotech’s experimental antibody drug for cancer. There’s a good reason for this: the large and expensive internal R&D organizations of Big Pharma companies like Sanofi haven’t been productive enough. Over the next several years Sanofi is facing patent expirations on some of its biggest sellers, such as anti-clotting drug clopidogrel bisulfate (Plavix) and the sleeping pill zolpidem (Ambien).

“We all know there is a patent cliff in this industry, and it goes from 2012 to 2014,” Viehbacher said. “But my goal isn’t just to fill a sales gap,” it’s to build a sustainable business. (Viehbacher spoke to Xconomy at length in June about his strategy for building sustainable business at Sanofi.)

Sanofi has been in Massachusetts for more than a decade, but the company has been less active in partnering with biotechs in the state than other Big Pharma outfits. The company conducts a wide variety of genomic research at its Cambridge Research Center on Albany Street, and last year the firm expanded its presence in the state with its acquisition of British vaccine developer Acambis, which has operations in Cambridge and Canton, MA. This year the company has formed alliances with …Next Page »

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PureTech Ventures says it has swelled its ranks with another Big Pharma veteran. John LaMattina, former president of global research and development at Pfizer, has joined the Boston-based venture firm as senior partner. PureTech has also promoted previous firm associates Eric Elenko and Steve Muniz to partner.

LaMattina—who retired from New York-based Pfizer (NYSE:PFE) in December 2007 after 30 years with the company—adds deep drug-development experience to PureTech. He’s even written a book on the topic of Pharma research and development called “Drug Truths: Dispelling the Myths About Pharma R&D.” His experience could have a major impact at PureTech, where partners and advisors use their experience to identify medical needs and then found companies to address those needs. (Many of our readers also know PureTech as the founding venture firm behind Follica, the developer of therapies to re-grow hair and treat baldness.)

PureTech has been known to recruit from the ranks of Big Pharma to lead its ventures or advise the firm on big opportunities in healthcare. For example, the firm previously recruited Eliot Forster, the former head of European R&D at Pfizer, to be CEO of its Cambridge, MA-based portfolio company Solace Pharmaceuticals. And PureTech’s own team includes Frank Douglas, another senior partner, who is the former chief scientific officer of drug giant Aventis (now Sanofi-Aventis). LaMattina, in fact, told me in an e-mail that one of the first things that caught his attention about PureTech was its track record in recruiting talented pharmaceutical executives.

“I was impressed by [PureTech’s] non-traditional model,” LaMattina told me. “Rather than wait for start-ups to come to them for funding, PureTech looks to key areas of medical need where they would like to invest, seeks out experts in that field, and does extensive research into where the next key breakthrough can be made.” (He noted that his early impression of the firm was also helped by the fact that this friend and former Pfizer colleague, Jeff Ives, is the CEO of PureTech portfolio company Satori Pharmaceuticals in Cambridge. He also mentioned Forster.)

Daphne Zohar, founder and managing partner of PureTech, said in a statement that LaMattina brings to the firm both his large network of industry and scientific contacts and his expertise in translating innovative technologies into products.

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PaxVax, a San Diego startup backed by Seattle’s Ignition Capital, has raised $2 million of a planned $6 million investment round, according to a document filed Friday with the Securities and Exchange Commission.

The biotech was founded in early 2007 to develop new oral vaccine technology based on a common cold virus called the adenovirus. The company says its vaccine, which is administered as oral tablets, avoids much of the requirements that conventional vaccines require—including cold storage for the vaccine itself and inoculation by qualified medical personnel. PaxVax says its oral tablets can be stored and distributed at room temperature, and are self-administered.

PaxVax says its vaccines also can be produced in large quantities and at record speed and low expense compared with traditional vaccines derived from egg culture. The company also says an oral vaccine may yield a more robust immune response than traditional vaccines.

The biotech was co-founded by Ken Kelley, who has worked in biotechnology for more than 25 years, including such companies as IntraBiotics Pharmaceuticals of Palo Alto, CA, and Integrated Genetics (acquired by Genzyme), and with such venture capital firms as K2 BioVentures and Latterell Venture Partners, according to the PaxVax website.

PaxVax’s board includes Ignition Capital operating partner Rennie Coit, who represents the Seattle VC firm at PaxVax. A pediatrician who got his medical degree at UC San Diego, Coit previously worked as a strategic planning consultant to clients that included academic medical centers, health insurance proviers, medical research organizations and global health providers. He also served as the chief operating officer of the University of Washington Medicine Neighborhood Clinics.

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TEDMED had Martha, Goldie, and other celebrity speakers, but San Diego-based Amylin Pharmaceuticals broke this week’s big news when it signed up a big Japanese partner to develop its line of obesity drugs. It’s all part of your regular dose of San Diego biotech news, and it’s ready now:

—Amylin Pharmaceuticals, the San Diego-based diabetes drug specialist, announced that it has formed a partnership with Japan’s Takeda Pharmaceuticals, which agreed to carry most of the development costs for Amylin’s weight-loss drugs. In return, Takeda gets a worldwide exclusive license to eventually commercialize Amylin’s experimental obesity drugs, including the combination of pramlintide and metreleptin, and davalintide.

—After a five-year hiatus, TEDMED founder Richard Saul Wurman, and president, Marc Hodosh (who also is an Xconomist), brought the conference on medical technology, entertainment and design to San Diego’s Hotel del Coronado. TEDMED announced during the conference, which included presentations by Boston Scientific co-founder (and Xconomist) John Abele, Martha Stewart, and Goldie Hawn, that the conference will return to the same location next October.

—I only had time to attend a fraction of the presentations at TEDMED last week. One of my favorites talks, though, was delivered by Bill Davenhall, who leads the health and human services marketing team at ESRI, the Redlands, CA, giant in geographic information systems. Davenhall talked about the importance of including patients’ “place histories” as part of their medical records and raised an interesting question: Will the electronic health record systems being created today have the capability to add data in new categories—such as “geo-medicine”–that aren’t typically included in today’s patient records?

—New York-based Xenomics filed a lawsuit against San Diego-based Sequenom that alleges Sequenom misrepresented the progress in its development of a prenatal test for Downs syndrome. Xenomix says it would not have licensed its patents to Sequenom had it known the truth.

—Denise profiled San Diego-based Sirigen, an early stage medical diagnostic company that is developing technology that uses light-emitting polymers to detect bits of DNA. Sirigen founder Brent Gaylord developed the technology at UC Santa Barbara, extending the significance of UCSB physicist and Nobel laureate Alan Heeger’s discovery of conductive polymers.

—The FDA told San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN) and its partner Eli Lilly the companies can now market exenatide (Byetta) as a frontline, standalone therapy for diabetes. The drug was previously approved for use with other drugs, or as a fallback option when other tretments failed.

—Vertex (NASDAQ: VRTX), the Cambridge, MA, biotech with operations in San Diego, said the latest trial of its telaprevir treatment for hepatitis C was able to attain the clinical definition of a cure in more than 80 percent of patients who got the drug. The finding is part of the mounting evidence Vertex is gathering on its quest to develop the first-of-its-kind protease inhibitor for the chronic liver disease.

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There’s big news about Enlight Biosciences breaking here at the Xconomy Forum: Pharma’s Bet on Boston Innovation. Abbott Laboratories (NYSE:ABT) has joined the consortium of big pharmas that are supporting Enlight, according to CEO David Steinberg; the Boston-based startup is out to develop platform technologies to help large drug companies like Abbott streamline the processes of developing new products and reduce the risk involved.

Abbott Park, IL-based Abbott, like the previous five pharmas to back Enlight, has agreed to provide Enlight with up to $13 million for its own operations and to invest in spinoff companies. Backers of Enlight’s innovative business model also include Merck & Co. (NYSE:MRK), Johnson & Johnson (NYSE:JNJ), Eli Lilly (NYSE:LLY), Novartis, and Pfizer (NYSE:PFE).

Enlight is addressing a major problem in the pharmaceutical industry—the tremendous risk and cost of developing a new drug. On average it takes more than $1 billion and about a decade to bring a drug to market. And the vast majority of drugs fail in clinical trials, often after the years and fortunes have been spent on them. Enlight is particularly interested is in developing platform technologies and tools that improve drug R&D but are not that actual drugs themselves, Steinberg said. The company’s goal is to launch companies to develop these technologies, which could ultimately be used by Enlight’s pharma company collaborators. Abbott’s contribution to Enlight brings the company’s total commitments from its pharma partners to $78 million.

“It’s further validation of our business model in terms of what is needed in pharma,” Steinberg said, adding that Abbott actually joined the collaborators at Enlight in the spring; the announcement has taken several months to get approved.

Enlight’s model is to hunt for innovation at the academic level and from companies; its pharma members get early access to the technologies that Enlight and they choose to invest in and develop. Each of the pharma members agree that they will share the technologies with each other—and eventually the drug-development industry as whole—to improve all of their chances of succeeding. PureTech Ventures of Boston was the founding venture investor in Enlight, which was launched in 2008. (Daphne Zohar, managing partner at PureTech, revealed earlier this afternoon during a panel here that Steinberg would be announcing the addition of a sixth pharmaceutical firm to the Enlight membership.)

“By putting the six pharmas together,” Steinberg said, “it expands tremendously what we can get done.” Enlight has already launched a startup called Endra, which develops technology that combines the capabilities of ultrasound with optical imaging to show drug developers whether a drug is able to shrink a tumor during clinical trials, rather than having to wait until after the study is completed.

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A number of New England’s life sciences companies had good news to report this week.

—Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ: VRTX) reported results from clinical trials that indicate its experimental hepatitis C drug, telaprevir, could work well for patients who haven’t responded fully to standard treatments, and could be as effective taken twice a day as it is taken three times a day. Luke explains what the news means for Vertex’s efforts to capture a share of the potentially huge market for hepatitis treatments.

—Medical device maker Interlace Medical of Framingham, MA, won FDA clearance to market its minimally invasive device for removing uterine fibroids and polyps.

—Burlington, MA-based CorNova raised $2.5 million of a proposed $6 million in equity financing, according to regulatory filings. CorNova is developing coronary stents with platinum surfaces.

—Anti-inflammatory drug developer Virdante Pharmaceuticals completed a second closing of its Series A financing round, bringing the total collected so far to $30 million. Thomas, McNerney & Partners led the deal, which was joined by Osage Partners, Biogen Idec New Ventures, Clarus Ventures, MedImmune Ventures, and Venrock Associates.

—Bedford, MA-based iRobot (NASDAQ:IRBT) launched a new healthcare unit. Under the direction of technology veteran Tod Loofbourrow, the unit will focus on developing robots to help seniors live independently.

—Pharma giant Novartis declined an option to continue development of a hepatitis C drug from Cambridge-based Idenix Pharmaceuticals (NASDAQ: IDIX). Idenix, whose stock dropped on the news, will seek another partner to back development of the drug, IDX184.

—RNA-interference drug developer Cequent raised $3.35 million in the first tranche of a venture round that could be worth as much as $15 million. The Cambridge-based startup is engineering E. coli bacteria to deliver RNAi molecules designed to combat a certain type of polyp in the colon.

—Pulmatrix raised $30.2 million in a Series B venture round led by Arch Venture Partners and Novartis Bioventures Fund and joined by Polaris Venture Partners and 5AM Ventures. The Lexington, MA-based startup is using technology from MIT and Harvard to prevent flu viruses and other pathogens from invading lung tissue.

—Cancer diagnostics developer On-Q-ity of Waltham, MA, reportedly raised $21 million in a Series A round of venture capital from Mohr Davidow, Bessemer Venture Partners, Physic Ventures and Northgate Capital. The firm was formed through the merger of CELLective Diagnostics and The DNA Repair Company, both Mohr Davidow Ventures portfolio companies.

—Ironwood Pharmaceuticals of Cambridge and its partner, New York-based Forest Laboratories (NYSE: FRX), said that Ironwood’s lead drug candidate, linaclotide, fared well in two pivotal clinical trials. The drug is designed to relieve chronic constipation; Luke has all (and I mean all) the details.

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“Ouch.” I’m sorry to say I didn’t write about the grand opening that drug giant Eli Lilly held in La Jolla yesterday for its new biotechnology center of excellence. I didn’t know about it.

I wrote last December about the difficulty of getting information from Lilly about the status of its plans to combine Applied Molecular Evolution and SGX, and suggested a more appropriate name for the facility might be “Lilly’s San Diego Biotechnology Center of Silence.” I was pleasantly surprised afterward when a Lilly media rep cordially reached out to provide contact information, and assured me that I’d be included when Lilly’s new eco-friendly center was opened. Oops.

It was my own fault, of course, for failing to spot the announcement that Lilly moved on the PR Newswire yesterday. What can I say? I got busy. Such is the nature of this business. The media demands a lot of hand-holding. (But then, Lilly did tell me I would be included.)

The center is officially known as the Lilly Biotechnology Center—San Diego. In its statement yesterday, Lilly says of the nearly 200 scientists based at the center, more than half are from AME, a local biotech that Lilly acquired in 2004 that specializes in biotechnology-based therapies built specifically from human proteins. Many of the rest are from SGX Pharmaceuticals, a San Diego startup that Lilly acquired in 2008 and merged into its discovery chemistry research and technology division.

I have to say I don’t have an excuse for this one either: In a speech in downtown San Diego today, Lilly’s chairman and CEO John C. Lechleiter declared that the engine of biopharmaceutical innovation is broken. In a statement released by Lilly, Lechleiter says, “At a time when the world desperately needs more new medicines—for everything from H1N1 to Alzheimer’s disease – we’re taking too long, spending too much and producing far too little.”

I’m sorry to report that I didn’t know about this in advance either.

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Europe’s drug regulators were not kind to a couple of Massachusetts biotech firms this week, but other New England life sciences companies had happier news to report.

—European drug regulators turned down Lexington, MA-based Antigenics’ bid for approval to market vitespen (Oncophage), a “cancer vaccine” for patients with kidney cancer. Shares of Antigenics (NASDAQ: AGEN) tumbled on the news.

—Ryan made a visit to the yeasty-smelling labs of Lebanon, NH-based Mascoma, where researchers are aiming to engineer microbes that can more efficiently produce ethanol from cellulose-rich materials such as wood chips, switch grass, and corn stalks. Mascoma is currently ramping up pilot production at a facility in Rome, NY, and hopes to complete one of the first commercial-scale cellulosic ethanol plants—in Kinross, MI—by 2012.

—Nuclea Biotechnologies raised $3.4 million in new equity financing. The Pittsfield, MA-based startup is developing genomic tools for cancer research and diagnosis.

—Ryan made the rounds of the big healthcare IT symposium put on by Partners HealthCare’s Center for Connected Health. The field is currently riding a wave of interest tipped off in part its inclusion in the economic stimulus bill, he explained, and the event attracted a mix of physicians, entrepreneurs, hospital administrators, academics, and technology executives. Ryan gave a great run-down of highlights from the event.

—Natalizumab (Tysabri), the multiple sclerosis drug from Cambridge, MA-based Biogen Idec (NASDAQ: BIIB), has reportedly come under fresh scrutiny from European regulators now that a total of 23 patients on the treatment have been diagnosed with a rare, potentially fatal brain infection called PML. According to Reuters, the European Medicines Agency has initiated a review to discuss any additional measures necessary to ensure the safety of the drug, which is also approved for Crohn’s disease. Shares of Biogen, and its partner Elan (NYSE:ELN) fell on the news.

—Wellesley, MA-based BioAssets Development Corporation inked a $30 million deal granting Frazer, PA-based Cephalon (NASDAQ: CEPH) to acquire the company. BioAssets will be eligible for various additional payments if Cephalon exercises the option and certain regulatory and sales milestones are reached.

—Boston-based American Well, provider of a Web-based system for remote medical consultations, raised $10 million in new equity funding, according to a regulatory filing. Investors in the round were not named.

—Luke gave a sneak peak of next week’s Xconomy Forum, which will explore how Big Pharma is seeking to boost its pace of innovation—and chances of success—in a notoriously risky industry. We’re all really excited about the event, which will include keynoters Deborah Dunsire, the CEO of Millennium: The Takeda Oncology Company, and Christoph Westphal, the CEO of Sirtris, and the senior vice president of GlaxoSmithKline’s Centre of Excellence for External Drug Discovery.

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From Australia comes word that San Diego-based Amylin Pharmaceuticals’ biggest drug, exenatide (Byetta), has been caught up in a controversy over a diabetes report co-sponsored by Amylin’s marketing partner, Eli Lilly & Co.

The study, compiled by researchers at the University of Canberra’s National Centre for Social and Economic Modelling (NATSEM), warned that 1.6 million Australians would be diagnosed with diabetes by 2050, according to an account in The Australian. Over the next 40 years, according to the study, people with type 2 diabetes would have 270,000 heart bypass operations, 250,000 strokes, and 750,000 cases of kidney complications.

Although the study mentioned exenatide, the generic name for Byetta, only in a footnote, it asserted that drugs in the same class as exenatide could produce greater health improvements for diabetic patients than exercise or existing drugs. And that seems to have sparked a bit of a controversy Down Under.

The newspaper reports that some experts were concerned that the report was part of a marketing push to win public subsidies for the medication. Australia’s Public Benefits Scheme recommended the drug for inclusion last year, but the federal government has yet to respond. This means exenatide is available only on private prescription at a relatively high cost. Consequently, it is not widely used.

NATSEM defended the integrity of the research, saying the projected increase in type 2 diabetes was a legitimate concern. Lilly was one of seven organizations to support the research. “As an independent research organization, the last thing we want to do is compromise our position, and for people to regard the position we are taking as biased towards the funding body,” NATSEM research director (health) Laurie Brown told the newspaper. The account came to my attention through the Pharmalot blog.

Lilly is responsible for developing and commercializing Amylin’s diabetes drug outside the U.S. The partnership agreement calls for Lilly to pay Amylin a royalty on non-U.S. sales after a one-time cumulative gross margin threshold amount is met. Amylin told investors in June that it expected to begin receiving royalty payments in 2010. Operating profits from exenatide sales in the U.S. are shared equally by the two companies. Amylin reported exenatide sales of $503.9 million for the first nine months of 2009, compared to $515.9 million during the same period a year earlier.

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There was a steady serenade of news from New England’s life sciences companies this past week, with both the startups and the public firms chiming in.

—Ryan profiled Boston BioCom, a Pfizer-backed startup aiming to commercialize life science discoveries from Russia. Based in, of course, Boston, the firm is also developing technology from the Massachusetts General Hospital lab of its chief scientific officer, Jeffrey Gelfand.

—Woburn, MA-based Flexion Therapeutics raised $33 million in a Series A financing led by Versant Ventures. 5AM Ventures and Sofinnova Partners joined in backing the company, which is out to reduce the time and expense required to take drugs from the earliest stages of development into initial clinical trials.

—Charles River Laboratories (NYSE: CRL) reportedly cut 115 positions at its Quebec-based subsidiary CTBR Bio-Research. Headquartered in Wilmington, MA, Charles River cut roughly 3 percent of its global workforce back in February.

—Jens Eckstein, a general partner in TVM Capital’s life sciences practice, went to Tokyo and came back with a message for the Boston life sciences community: “We should cherish what we have and work hard to keep things intact and healthy.”

—Lexington, MA-based Cubist Pharmaceuticals (NASDAQ: CBST) teamed up with Cambridge, MA-based Hydra Biosciences to develop new pain medications. Cubist will pay Hydra $5 million upfront, and provide $5 million in R&D funding annually for two years.

—Augmenix of Waltham, MA, raised $6.1 million in a Series B financing round to support the development of its technology for reducing tissue damage during radiation treatment. Ascension Health Ventures led the round; Versant Ventures, Pinnacle Ventures, Catalyst Health Ventures, and several private investors participated as well.

—Drug developer Synageva BioPharma, also of Waltham, raised $12 million, completing a $45 million round of financing. New Leaf Venture Partners, a new investor, and return investors contributed to the round.

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Research published today has revealed the existence of a new San Diego life sciences company that is working to commercialize anti-cancer technologies intended to boost the immune system to resist tumor growth.

A paper in the journal PloS ONE shows that a gene for a specially engineered form of a protein called CD40 ligand (CD40L), developed by former researchers from UC San Diego, can be used to activate the immune system to fight tumors in mice. The team delivered the gene using nanoparticles created by cancer researchers at the Massachusetts Institute of Technology. The technique can boost the immune response even more when combined with bacterial products called Toll-Like Receptor activators.

The new form of CD40L, called UltraCD40L, is the lead drug candidate for Multimeric Biotherapeutics, a San Diego biotech startup that was founded in February 2008. The startup had made presentations at the Tech Coast Angels’ recent fast pitch competition and Biocom’s investor conference, but was not widely known prior to the publication of the PloS One paper. UltraCD40L was developed at UCSD by Richard Kornbluth, a former associate professor of medicine who left to start Multimeric Bio with Marc Hertz, who is the CEO, and Antonella Vitiello, the startup’s principal scientist.

In an e-mail last night, Kornbluth told me that Multimeric Bio is a pre-seed stage company that has been self-funded by the founders with help from angel investors. (Multimeric refers to a protein with multiple polypeptide chains.)

“From over 9,000 published papers, CD40L has emerged as one of the most powerful immune molecules produced by the body,” Kornbluth says. Researchers haven’t been able to use the molecule as a drug until now because they didn’t realize that it needed to be packaged as aggregated multimeric molecules to be active in the body.

Kornbluth says the easiest way to introduce UltraCD40L, which is a large protein, into the body is to deliver short strands of DNA, called plasmid DNA, that direct its synthesis inside cells. However, the expression of genes from injected DNA is inefficient, especially when the DNA is injected directly into tumors. So the San Diego team collaborated with scientists at MIT’s David H. Koch Institute for Integrative Cancer Research at MIT. The MIT team, which includes Robert Langer (a Boston Xconomist), Gregory Zugates, and Daniel Anderson, have developed biodegradable polymer nanoparticles that encapsulate the DNA and deliver it directly into tumors so that the protein encoded by the gene can be strongly expressed.

The research reported today, Kornbluth says, “describes the use of these polymers to deliver UltraCD40L into large melanoma tumors in mice, causing the tumors to shrink and curing many of the mice completely.”

Kornbluth says the significance of today’s research findings for Multimeric Bio is that it shows the potential application of its UltraCD40L drug candidate in cancer immunotherapy in humans. “The company has applied for grant support to help move this technology to the clinic,” he says, and Multimeric Bio “is especially interested in partnering with a larger company for this purpose.”

Kornbluth says Multimeric Bio is the exclusive licensee of the technology he developed when he was at UCSD. Apart from the cancer immunotherapy work, he says previous reports on UltraCD40L have also shown that is a highly effective vaccine adjuvant, meaning that it can dramatically increase the strength of an otherwise ineffective vaccine. He says it’s currently being tested as part of an HIV vaccine in the monkey model for AIDS.

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It’s been a short week and a long weekend since last I rounded up New England’s life sciences news, but there were still a few stories worth mentioning.

—Luke took an in-depth look at giant Amgen’s (NASDAQ: AMGN) efforts to boost its rate of success in getting new drugs to market. Though Amgen is based in Thousand Oaks, its 200-person-strong outpost in Cambridge, MA, plays an important role in its R&D operation.

—Ernst & Young released a sweeping analysis of the medical device industry that indicated that it’s a challenging time for device firms, particularly the smaller players that develop many of the new technologies the industry depends on for growth. Fundraising was down 53 percent among U.S. device companies, M&A activity was down by 41 percent, and the IPO market was flat-lining, according to the report.

—In contrast, our friends at ChubbyBrain sent us the data on September startup funding and the news for life sciences as a whole was fairly rosy. That sector accounted for $98.8 million of the $228 million total raised by Massachusetts companies that month.

—Cambridge-based Alkermes (NASDAQ: ALKS) reported that its anti-addiction drug, ALKS 33, was well-tolerated and able to block the effects of the powerful opioid painkiller remifentanil (Ultiva) long enough to enable once-daily dosing. Based on those results, from a pair of early-stage clinical trials, Alkermes is preparing for a mid-stage clinical trial of the drug, to start before the end of this year.

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The storm may not have entirely passed, but the venture capital industry unbattened the hatches during the three months that ended in September. At least that’s the sense I get from a 69-page report on U.S. venture investing, which we get from New York-based ChubbyBrain, an information services firm developing tools for investors, startups, and aspiring entrepreneurs.

In its “Pulse of the Innovation Economy” report, ChubbyBrain says just over $6 billion in venture capital funding was invested in 680 deals nationwide. That’s down almost 16 percent from the $7.2 billion that VC firms invested in privately held companies during the third quarter of 2008, but a 14 percent increase in deployed capital compared with the previous quarter of this year. It’s a sign that technology-based startups are gaining increased momentum from the winter of ‘09, especially considering the increased valuations in public markets that even includes some IPOs, such as the recent public offering of Watertown, MA-based A123Systems. The report notes that the momentum for venture investments picked up during the quarter, with September accounting for 40 percent of the deals nationwide.

California—and especially Northern California—remains in a class by itself for venture activity, according to the report. Just over half (51 percent) of the total number of deals went down in the Golden State (along with 56 percent of the total capital invested, or $3.4 billion). California was followed by Massachusetts, Texas, New York, and Georgia. The state of Washington ranked No. 7 on the ChubbyBrain list of top 10 states for venture activity.

Two Xconomy cities also placed among the top 10 nationwide in terms of overall VC funding and deal activity. San Diego, which had 28 deals totaling $280 million, ranked third overall, behind …Next Page »

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It was a busy week in the land of New England life sciences. Let’s dive in.

—Luke did a massive analysis of the financial health of all the public biotech companies we follow the Boston area and the news… Well, it wasn’t good.

—Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ:VRTX) brought in $155 million in cash by selling $120 million in debt and $35 million for the rights to potential milestone payments. Both deals were related to the potential European commercialization of telaprevir, Vertex’s experimental drug for hepatitis C.

—Adimab, a Lebanon, NH-based biotech startup developing a new platform for discovering antibody drugs, raised $8.2 million in a Series D round of venture financing. Google Ventures led the financing and Polaris Venture Partners, SV Life Sciences OrbiMed Advisors, and Borealis Ventures participated as well.

—Merrimack Pharmaceuticals of Cambridge forged a co-development and co-marketing deal with French pharmaceutical firm Sanofi-Aventis. The partnership, focused on Merrimack’s antibody cancer drug MM-121, will bring the Cambridge firm $60 million upfront and as much as $470 million more in milestone payments, not to mention double-digit percentage royalties, should the drug reach the market.

—Luke chatted with Peter Hecht, CEO of Cambridge -based Ironwood Pharmaceuticals, which recently recruited former Genentech CFO David Ebersman to its board. Does the move signal that Ironwood—whose lead, potential blockbuster, drug is in late-stage clinical trials—is preparing to go public? Hecht wouldn’t say so, but Luke explains why Ironwood might fare well on Wall Street.

—The FDA followed an earlier advisory panel recommendation that clofarabine (Clolar), a leukemia drug from Genzyme (NASDAQ: GENZ), not be approved for use in a broader population of patients. The agency said that Cambridge-based Genzyme should conduct another trial of the drug in patients over age 60; it’s currently approved just for children with leukemia.

—Ryan spent the day at the MassBio Investors Forum in Boston, checking in with folks from Cambridge-based RNAi-drug developer Alnylam Pharmaceuticals (NASDAQ:ALNY), (which referenced a potential spin-off company perhaps in the works); Waltham, MA-based EyeGate Pharma (which has rounded up $12 million of a planned $20 million to $25 million financing); Cequent Pharmaceuticals, another Cambridge-based RNAi-drug developer (which is moving its first drug into clinical trials); and Pathogenica (a brand-new diagnostics firm spun out of George Church’s lab at Harvard Medical School). He also gleaned some insights (and arguments) about the future of biotechnology from Harvard Business School professor Gary Pisano and life sciences investment firm CEO Steven Burrill.

—Epizyme, a Cambridge startups out to turn the science of epigenetics into new drugs that work by turning genes on and off, raised $32 million in a Series B venture round led by Bay City Capital. Amgen Ventures, Astellas Venture Partners, MPM Capital, and Kleiner Perkins Caufield & Byers participated as well.

—Boston-based antibiotic developer Paratek Pharmaceuticals struck an exclusive development and commercialization deal with Swiss drug giant Novartis. The deal, which could be worth as much as $485 million in initial milestone payments, focuses on Paratek’s PTK 0796, which is in late-stage clinical development for treating complicated skin and skin structure infections as well as certain cases of pneumonia.

—Immuneering, which is developing computer models to predict patients’ responses to cancer drugs, became the first life sciences startup to join Polaris Venture Partners’ new Dog Patch Labs startup incubator in Cambridge. The move will take the company out of CEO Ben Zeskind’s apartment in Boston’s Back Bay.

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The life sciences news was relatively light over the last week, except perhaps for Sequenom, the medical diagnostics company that has yet to publicly disclose much about its misconduct in handling clinical trial data.

—Sequenom (NASDAQ: SQNM) disclosed that it met with the FBI and the U.S. Attorney’s Office in San Diego in connection with the company’s mishandling of data from a clinical trial for its Down syndrome prenatal test. This latest development came a week after a five-month internal investigation led the company to fire CEO (and San Diego Xconomist) Harry Stylli along with three others. The company said it is cooperating fully with government investigators and the dismissed employees had denied wrongdoing.

—Accumetrics reeled in another $16.5 million from existing investors, including Essex Woodlands Health Ventures and Kaiser Permanente Ventures. As Bruce reported, the company sees a multibillion-dollar market for its diagnostic device that calibrates the right dosage of anti-clotting drugs.

—Transdel Pharmaceuticals (OTC BB: TDLP) saw mixed results from a clinical trial of its topical pain reliever. The cream containing ketoprofen was better than a placebo among patients who used the cream as directed, but had no advantage among patients who applied the cream incorrectly, or failed to follow the study protocol. CEO Juliet Singh told Luke the trial was a success and that the FDA would consider the two sets of data.

—Marval Biosciences, San Diego’s latest virtual biomedical startup, raised $2.5 million in venture financing from DFJ Frontier in Los Angeles and DFJ Mercury in Houston, affiliates of the Silicon Valley firm Draper Fisher Jurvetson. The company is working on next-generation contrast agents for medical imaging.

—LifeModeler of San Clemente, CA had a cameo in one of the biggest science stories of the week. The company’s biomechanical visualization software was used to determine how Ardi, a 4.4-million-year-old hominid fossil, walked and moved. Orthopedic surgeons use the software to plan and practice joint-replacement surgeries,

—Gen-Probe (NASDAQ: GPRO), which uses nucleic acid testing of blood samples to diagnose human diseases, agreed to pay $60 million in cash to acquire Wisconsin-based Prodesse, which is developing sophisticated reagents that can rapidly identify certain types of respiratory viruses, intestinal bacteria, and other infectious microbes.

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As has been the case in recent weeks, M&A news featured prominently in this week’s New England tech and life sciences deals.

—Harvard spinoff Tetraphase Pharmaceuticals of Watertown, MA, raised $10 million out of a planned $29.6 million equity financing round, the company indicated in an SEC filing. Tetraphase is developing new antibiotics to treat drug-resistant infections.

—Norwalk, CT-based Xerox (NYSE: XRX) said it will acquire Dallas, TX-based business process outsourcing firm Affiliated Computer Services (NYSE: ACS), a, for $6.4 billion in cash and stock.

—Software maker Egenera of Marlborough, MA, raised $3 million in new equity financing. Existing investors including Austin Ventures, Crosslink Capital, Kodiak Venture Partners, Pharos Capital Group, and Technology Crossover Ventures contributed to the round, according to Mass High Tech.

—Aspect Medical Systems (NASDAQ:ASPM) of Norwood, MA, agreed to be acquired by Irish healthcare products giant Covidien (NYSE:COV) for some $210 million in cash. Aspect’s brain monitoring equipment will become part of Covidien’s Oximetry and Monitoring product line.

—Acton, MA-based Blackwave, a provider of Internet-video servers, took in $3.5 million of a planned $9.1 million round of equity financing from undisclosed investors. Flybridge Capital Partners, Globespan Capital Partners, and Sigma Partners have participated in previous funding rounds for the company.

—Taiwan’s Prime View International (PVI) sweetened the deal in a proposed merger with E Ink, and shareholders of the Cambridge, MA-based firm complained that PVI’s initial offer of $215 million in cash was too low. Under the terms of the new deal, E Ink shareholder would get 120 million shares of preferred stock in the combined company, in addition to the $215 million.

—Cambridge-based Vertex Pharmaceuticals (NASDAQ:VRTX) inked a pair of debt deals related to European commercialization of its hepatitis C drug, telaprevir, that will bring in $155 million in cash. Ryan has the details on the deals and the drug’s prospects.

—Google Ventures led a Series D financing round for Lebanon, NH-based Adimab, which is developing a fast and powerful platform for discovering new antibody drugs. Other investors in the deal, the value of which was not disclosed, include return backers Polaris Venture Partners, SV Life Sciences, OrbiMed Advisors, and Borealis Ventures.

—Merrimack Pharmaceuticals of Cambridge, MA, inked a deal with French pharmaceutical giant Sanofi-Aventis giving Merrimack $60 million up front, plus as much as $470 million in potential milestone payments, in return for rights to co-develop and co-market MM-121, an experimental antibody drug for cancer.

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