Clinical trial results and drug collaborators made up the New England life sciences news this week.

—New Jersey-based drugmaker Merck announced backing a few Boston-area companies in the past few weeks. Its Global Health Innovation Fund led a $10 million financing for Cambridge, MA-based Daktari Diagnostics, a developer of technology for testing small quantities of blood and other fluids that it hopes can monitor HIV patients in the developing world. And Merck pledged $17 million to Marlborough, MA-based Physicians Interactive Holdings. The company will put the money towards developing its online and mobile tools to connect doctors and pharmaceutical companies.

—An experimental drug from Cambridge-based Alnylam Pharmaceuticals (NASDAQ: ALNY) helped lower so-called bad cholesterol by an average of 39 percent at the highest dose studied in a small clinical trial.

—Aveo Pharmaceuticals (NASDAQ: AVEO) of Cambridge said it met it goals in a clinical trial called TIVO-1 of its experimental drug for treating kidney cancer. In the study of 517 patients, Aveo’s tivozanib was able to keep tumors from spreading a median of 11.9 months, compared with 9.1 months for another drug in its class from Bayer and Onyx Pharmaceuticals. It was a narrow victory, though, as the trial’s goal was to show the Aveo drug kept tumors from spreading about an extra three months.

—Weston, MA-based Biogen Idec (NASDAQ: BIIB) said it will pay Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) up to $299 million for collaborating on a treatment for a spinal muscular atrophy, a rare disorder found in newborns.

—Inspiration Biopharmaceuticals moved into its new digs in Kendall Square, after more than seven years of operating as a virtual biotech company that’s pursuing hemophilia treatments. It was founded by hedge fund manager John Taylor and Scott Martin, a Texas energy veteran whose son has hemophilia.

—The founders of Sermo, a Cambridge-based provider of an online community for doctors, are moving on to a new spinoff called par8o, the online publication Pharmalot reported. CEO Daniel Palestrant and chief medical officer Adam Sharp say on the par8o website that the new company will be focused on more efficiently connecting doctors and patients.

—Watertown, MA-based Forma Therapeutics inked a deal with Germany-based Boehringer Ingelheim that provides $65 million in upfront cash and four years of R&D support for discovering cancer drugs. Forma, which now has seven partnerships with heavy hitters, could also get potentially $750 million more from Boehringer Ingelheim as the cancer drugs move through development.

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

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

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

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

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

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

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Cambridge, MA-based Cerulean Pharma announced today that it has raised $15 million in a Series D financing round, which included one new investor: CVF, an affiliate of Henry Crown and Company. Also participating in this round were existing investors Polaris Venture Partners, Venrock, Lilly Ventures, Lux Capital, and Bessemer Venture Partners.

Cerulean’s lead drug candidate, CRLX101, is a “nanoparticle”—a tiny chemical package designed to burrow its way into cancer cells and kill them. In July, the company began a new Phase 2 trial of the drug in non-small cell lung cancer. The company plans to release top-line results from that trial next year.

Cerulean says it will use the new money to support the completion of that trial, as well as several others that will take place at academic medical centers. The company also plans to expand its platform to other opportunities, including RNA-based therapeutics.

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We’ve seen life sciences headlines from a mix of established drugmakers and universities in New England this week.

—Waltham, MA-based Repligen is picking up a unit of the Danish industrial-biotech products maker Novozymes A/S for about $22.7 million in cash. Repligen (NASDAQ: RGEN) could also pay another roughly $5.6 million to the unit, Novozymes Biopharma Sweden, which makes proteins used in the large-scale production of biotech drugs.

—Drug developer Alnylam Pharmaceuticals inked a partnership deal with GlaxoSmithKline (NYSE: GSK) surrounding its RNA interference technology for improving vaccine production. The technology, called VaxiRNA, uses small molecules to silent specific genes that limit the efficient growth of viruses in vaccine manufacturing systems. The exact value of the deal wasn’t disclosed, but Alnylam (NASDAQ: ALNY) will receive funding, potential milestones, and payments on product sales if the technology leads to an approved product.

—The Who’s Roger Daltrey, Aerosmith’s Steven Tyler, and actress Julie Andrews are funding an effort by MIT professor Bob Langer and Harvard University surgeon Steven Zeitels to develop a vibrating gel that would revive damaged vocal cords. It could treat both singers and throat cancer patients, and is scheduled to enter its first clinical trial in 2012.

—Verastem, a 15-month-old startup with no drugs yet in clinical trials, filed for an initial public offering. The Cambridge-based company—led by CEO Christoph Westphal and founded on science from MIT’s Bob Weinberg and Eric Lander—is developing treatments focused on cancer stem cells, sometimes known as “tumor-initiating” cells. It raised $32 million this July and is targeting $50 million more with the IPO.

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Cambridge, MA-based Alnylam Pharmaceuticals (NASDAQ: ALNY) announced today that it has formed a collaboration deal with GlaxoSmithKline (NYSE: GSK) centered around an RNAi technology Alnylam developed to enhance vaccine production. The technology, called VaxiRNA, uses molecules called “small interfering RNAs” (siRNAs) to silent specific genes that limit the efficient growth of viruses in vaccine manufacturing systems.

The financial worth of the partnership was not disclosed, though the announcement does say that under the terms of the agreement, “GSK will provide funding and certain milestone payments to Alnylam.” If a commercial product emerges from the partnership, Alnylam will receive payments on unit product sales.

The agreement comes just a year after a string of partnership disappointments for Alnylam. Last September, Novartis ended a partnership with Alnylam, and two months later, Roche pulled out of RNAi all together, which also involved ending a program with Alnylam. But Alnylam CEO John Maraganore never lost his enthusiasm for the technology. In a tweetchat with Xconomy on October 5, he was asked why he thought so many people had soured on RNAi—a technology that had long been considered a promising method for turning off disease-causing genes but that has yet to yield a marketable product. His response: “people/companies are waiting for clinical data, which is what we are focused on.”

Alnylam announced the partnership a few hours in advance of its third-quarter financial results. Wall Street analysts, on average, are expecting the company to report a loss of 35 cents per share on sales of $20.5 million. No doubt analysts who listen in on the earnings call, which is scheduled for 4:30 p.m. today, will be eager to hear management’s take on what the Glaxo partnership means for the future of the company—and for RNAi as a whole.

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

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

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

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

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

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

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

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

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

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

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

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Today, Worcester, MA-based RXi Pharmaceuticals (NASDAQ: RXII) announced that it will split into two publicly traded companies. The first, called Galena Biopharma, will focus on developing targeted cancer therapies and will be headquartered in Portland, OR. RXi will be spun off later this year and will continue to work on RNAi-based therapeutics—the company’s original mission when it was founded in 2003.

The split is not entirely surprising. RXi was founded around the work of Dr. Craig Mello, a professor of molecular medicine at the University of Massachusetts Medical School, and a Nobel Prize winner for his work in “RNA interference”—molecules that silence disease-causing genes. But RNAi therapeutics have been slow to realize their potential, and in an interview a few days before today’s announcement, RXi CEO Mark Ahn acknowledged that the company recognized a need to find a quicker path to revenues and profitability. “Shareholders were demanding progress in moving our company forward,” he says. “We knew how to deliver complex peptides to cells. We thought we could leverage that to go from just a research-platform company to a drug-development company.”

So Ahn and his team focused on transforming RXi into a developer of peptide immunotherapies—protein-based drugs that stimulate the immune system. RXi started that process in March, when it bought Apthera, a Scottsdale, AZ-based developer of a therapeutic cancer vaccine, E75 (NeuVax), which is being developed to treat breast cancer. Apthera completed a successful Phase 2 trial, but the time of the RXi acquisition, the FDA had a clinical hold on E75 because of manufacturing concerns, Ahn says. RXi completed additional work that the agency required, he says, and the clinical hold was lifted on Sept. 12. The company plans to start the pivotal Phase 3 study in the first half of 2012.

On September 26, RXi further boosted its pipeline of cancer vaccines by licensing a molecule from the University of Texas MD Anderson Cancer Center and Henry M. Jackson Foundation for the Advancement of Military Medicine. The vaccine targets Folate Binding Protein-E39 (FBP), which is over-produced in more than 90 percent of ovarian and endometrial tumors. “FBP is exciting for us because it’s a very well-validated target in cancer care,” Ahn says. “It’s heavily over-expressed in gynecological cancers, but not in normal tissues. That ratio makes it an ideal target.” The company plans to take the vaccine into Phase 1 studies by the end of this year.

Both cancer vaccines are now under the umbrella of Galena. As for RXi, it will continue to develop RXI-109, an RNAi-based drug to treat scarring and fibrosis. The company said in a statement about the spinoff that RXi will also study “the therapeutic potential of gene silencing more broadly,” perhaps by partnering with other parties interested in RNAi.

Investors will clearly take some convincing, though: RXi’s stock dropped 23 percent to 76 cents per share on the announcement.

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

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

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

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

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

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

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

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

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

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

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

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

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

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[Updated 8/15/11 8:00 am. See below.] In mid-July, Cambridge, MA-based Cerulean Pharma began a new clinical trial of its cancer drug CRLX101, which is a “nanoparticle”—a powerful chemical wrapped in a tiny package that can burrow its way into cancer cells and kill them. Cerulean is one of a handful of companies laboring to apply nanotechnology to drug delivery. The trial, which will involve 150 patients with non-small cell lung cancer, should shed some light on the potential of nano-drugs in the cancer setting when top line results are released next year.

But CEO Oliver Fetzer isn’t waiting for proof that Cerulean’s approach works. He’s so optimistic that he has already set his sights on a big new opportunity for the company’s tiny drug platform: RNA interference (RNAi). About a decade ago, the pharmaceutical industry started pouring research dollars into RNAi—a new method for shutting off disease-causing genes and proteins. But there was a problem. “If you just inject RNA into the patient, enzymes degrade it very quickly,” Fetzer told Xconomy in a recent sit-down interview. So last year, Cerulean started testing its nanoparticles to see if they might offer a better way to deliver RNAi therapeutics.

Cerulean isn’t the only company to spot an opportunity for nanoparticles in RNAi. On July 25, Cambridge-based Alnylam Pharmaceuticals (NASDAQ: ALNY)—one of the pioneers in RNAi—announced that it and its collaborators at the Massachusetts Institute of Technology discovered novel nanoparticles that might facilitate the delivery of RNAi drugs directly into cells. Alnylam is developing RNAi approaches for several diseases, including cancer.

The difficulty of translating the promise of RNAi into drugs has been a major downer for the field. Last November, Swiss drug giant Roche unexpectedly pulled the plug on its RNAi program, which included ending a research alliance with Alnylam that once had the potential to earn the Cambridge company … Next Page »

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When Cambridge, MA-based Alnylam (NASDAQ: ALNY) made its debut last year at the annual American Society of Clinical Oncology (ASCO) conference, it only had a pittance of safety data on its drug, which is designed to treat advanced solid tumors that have spread to the liver. At this year’s conference, which starts June 3 in Chicago, Alnylam CEO John Maraganore hopes the company will make more of a splash, especially since one of the patients in the trial being presented has been on its cancer drug for more than a year.

Maraganore can’t reveal much about that patient until the ASCO presentation on June 4, but it’s clear he’s excited she’s done well on the experimental drug, called ALN-VSP02. “This patient failed all other therapies,” he says. “As long as she’s responding, she’ll continue to receive our drug.”

ASCO could end up being a much-needed bright spot in what has been a tough year for Alnylam. The company has three drugs in clinical trials based on the technology RNA interference (RNAi), a once-hot technique that involves silencing key genes involved in a range of diseases. But last September, Novartis ended a partnership with Alnylam. Two months later, Roche pulled out of RNAi all together, which also involved axing a program with Alnylam.

Then in mid-March, seemingly out of the blue, Alnylam partner Tekmira (NASDAQ: TKMR)—which which provides a key nanoparticle technology used in ALN-VSP and other RNAi drugs—sued Alnylam for trade-secret violations. All told, Alnylam’s stock has lost 34 percent of its value during this string of events, falling from nearly $15 last September to a recent $9.68 at yesterday’s close.

But Maraganore hasn’t lost faith in Alnylam—or in RNAi as a potential game-changer. “I’ve seen this play out before,” says Maraganore, who met with Xconomy New York when he was in town on May 25 for the ThinkEquity Healthcare Conference. He points out that the pharmaceutical industry once abandoned monoclonal antibodies. Then the biotech industry picked up the ball and monoclonals became the fastest-growing category in all of pharma. “The driver for RNAi is going to be clinical data,” Maraganore says. “When it happens, you’ll see pharma come back.”

Maraganore says that the Phase 1 data being released at ASCO will be the first of three key datasets Alnylam plans to release this year. In the third quarter, the company will present data from its trials of ALN-TTR, which treats a rare hereditary disease called TTR-mediated amyloidosis. And in the fourth quarter, it will release clinical data from … Next Page »

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Cambridge, MA-based Alnylam Pharmaceuticals (NASDAQ:ALNY) has found another partner to help it deliver its gene-silencing drugs to tissues deep in the body. Precision NanoSystems, of Vancouver, British Columbia, has agreed to lend Alnylam its expertise in using its so-called small lipid nanoparticles to potentially deliver RNA-interference (RNAi) drugs, the companies said today. The tiny particles could help advance Alnylam’s gene-silencing drugs through the liver, which has proved a difficult barrier to homing in on tissues deeper in the body with such treatments.

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This week we’ve seen news of acquisitions and funding, as well as longer articles on strategy and research moves for New England’s life sciences firms.

—BL Healthcare, a provider of telemedicine products that is based in Foxboro, MA, has bumped its Series A funding round up to $4.9 million, with another $2 million in equity-, debt-, and rights-based financing, an SEC filing showed.

—Luke took a look at the moves that Cambridge, MA-based Epizyme has been making in scoring deals with Big Pharma companies. GlaxoSmithKline (NYSE: GSK) paid the three-year-old biotech $20 million upfront with potentially another $630 million in milestones for a drug discovery partnership, and Japanese firm Eisai Pharmaceuticals will pump $6 million upfront and potentially $200 million in milestones into Epizyme for a collaboration to develop cancer drugs.

—Cambridge-based Vertex Pharmaceuticals (NASDAQ: VRTX) said the Phase III study of its cystic fibrosis drug, VX-770, met its primary goal among patients ages 6 to 11 of improving lung function through 24 weeks, showing that the drug is working about as well in children as it did in older patients with the genetic disorder. The 48-week study of 52 patients is still ongoing, but at 24 weeks, children on the drug showed a mean absolute improvement from baseline in lung function of 12.5 percent.

—Follica, the baldness treatment developer that got started in Boston in 2006, is working to protect its technology that uses lithium treatments to stimulate new hair growth with a patent application, filed in September and published this March. But that’s only one piece of the multiple areas of research that Follica is focusing on, CEO and president William Ju told Ryan.

—Worcester, MA-based RNA interference drug developer RXi Pharmaceuticals (NASDAQ: RXII) announced it has agreed to acquire Scottsdale, AZ-based Apthera, a developer of peptide immunotherapies for cancer. Apthera shareholders will get 4.8 million of RXi’s shares, which were valued at $1.50 before the deal. As part of the agreement, RXi CEO Noah Beerman will resign and will be replaced by RXi board member Mark Ahn.

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We had plenty of headlines from New England area drug companies this week, with news of clinical trial results, technology developments, lawsuits, and funding.

—The FDA set April 28 as the date that an advisory committee will meet on Cambridge, MA-based Vertex Pharmaceuticals’ (NASDAQ: VRTX) application for approval of telaprevir, its experimental drug for hepatitis C. The federal agency, which often follows the recommendations of such advisory groups, will likely decide on the drug’s approval application on May 23, Vertex said.

—Cambridge-based Alnylam Pharmaceuticals (NASDAQ: ALNY) has been working since 2006 with Vancouver, BC-based Tekmira Pharmaceuticals, matching its RNAi therapy with Almira’s drug delivery technology, but Tekmira filed a lawsuit against Alnylam stating the Cambridge company has committed misappropriation of trade secrets as part of the partnership. My colleague Luke interviewed Alnylam CEO John Maraganore to get his take on the litigation.

—Synageva BioPharma of Lexington, MA, nabbed $25 million from its previous lead investors to fund its pipeline of drugs for treating rare diseases. The company is in early clinical development with its lead drug, SBC-102, which is intented to replace the enzyme called lysosomal acid lipase; deficiencies of the enzyme cause fatty materials called lipids to accumulate in tissues throughout the body, leading to gastrointestinal, liver, and cardiovascular complications.

—Vismodegib, a drug being developed by Lexington-based Curis (NASDAQ: CRIS) and South San Francisco-based Genentech, met its primary endpoint of tumor shrinkage in a study of patients with an inoperable form of severe skin cancer called advanced basal cell carcinoma. Roche, which owns Genentech, indicated it plans to submit an application for regulatory approval of the drug sometime this year, Curis said.

—Still River Systems, a Littleton, MA-based maker of proton therapies for treating cancer, raised $11.5 million. And Marlborough, MA-based medical devices firm CardioFocus pinned down a $5 million debt-based financing from Silicon Valley Bank.

—Peptimmune, a Somerville, MA-based company bought by Genzyme in 1999 and spun out by the biotech in 2002, filed for Chapter 7 liquidation this week. The company has about $2 million in assets and $2.2 million in liabilities, and has raised about $100 million in equity and debt.

—My colleague Ryan wrote about the advances that Cambridge-based VBI is making in addressing a major challenge in the vaccine field, by developing thermostable vaccines, which don’t need to be stored in freezing or cool temperatures.

—PerkinElmer, a Waltham, MA-based provider of life sciences tools and services, inked an agreement to buy CambridgeSoft, a Cambridge-based supplier of software and scientific databases to life sciences and biotech companies. PerkinElmer said it paid about $220 million total for that purchase and the acquisition of Research Triangle Park, NC-based ArtusLabs.

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A week after settling litigation related to the patents on gene-silencing treatments, Alnylam Pharmaceuticals and others have found themselves in another legal battle over the Tuschl patents related to RNA-interference treatments. This time the University of Utah has named Cambridge, MA-based Alnylam (NASDAQ:ALNY), Max Planck, the Whitehead Institute for Biomedical Research, MIT, and the University of Massachusetts in a civil complaint filed in federal court in Massachusetts on Tuesday, Alnylam said in a regulatory filing.

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Cambridge, MA-based Alnylam Pharmaceuticals (NASDAQ:ALNY) has been working with Tekmira Pharmaceuticals (TSE:TKM) of Vancouver, BC, since at least 2006 on getting its gene-silencing drugs into cells to treat diseases. But the partnership has gone sour. Tekmira has filed a lawsuit that is seeking what could amount to more than $1 billion from Alnylam.

Alnylam, founded in 2002, has been a leader in technology that uses RNA molecules to silence certain disease-related genes. While these drugs hold promise because of their ability to specifically target genes in ways other drugs can’t, the new RNA medicines require special help so they can be effectively delivered to the right place in cells. Alnylam has relied heavily on partners such as Tekmira, which has developed particles to carry gene-silencing compounds in the bloodstream and deliver them to the desired cells. Tekmira, for example, provides the carrier particles (a.k.a lipid nanoparticles) that Alnylam uses for its key experimental drugs for liver cancer (ALN-VSP) and TTR-mediated amyloidosis (ALN-TTR). Tekmira has received more than $45 million in funding from Alnylam through the companies’ partnership activities, and Tekmira stands to gain more money from Alnylam’s potential sales of drugs that use Tekmira’s technology, according to the companies.

Alnylam has filed patents on new carrier particles for RNAi drugs, listing Alnylam scientists as the inventors, according to Alan Carr, a biotech analyst at Needham & Company, who covers Alnylam’s stock. Presumably, if these patents are awarded, Alnylam wouldn’t have to pay Tekmira to develop drugs with particles invented by Alnylam scientists. Yet in its complaint filed this week in the Business Litigation Session of the Massachusetts Superior Court, Tekmira “alleges that Alnylam is claiming … that Alnylam has developed novel siRNA delivery formulations and lipids that can be obtained from Alnylam instead of Tekmira. Tekmira … alleges… that these purported Alnylam formulations and lipids are actually based on, and in whole or in part developed from Tekmira’s technology.”

“It comes down to inventorship on some patent applications filed by Alnylam,” Carr said. “And Tekmira believes that they contributed to it and that they should have at least partial ownership of it.”

Tekmira announced its litigation against Alnylam after the close of the market on Wednesday. At the close of the mark on Thursday, Tekmira’s shares were down about 10 percent to $3.96 and Alnylam’s shares fell almost 3 percent percent to $9.86. Tekmira has a lot at stake in this case, given how much of its future revenue depends on income from its drug-delivery technology through partners like Alnylam. In addition to Tekmira, Alnylam has worked on methods of delivering its gene-silencing treatments with AlCana Technologies, The University of British Columbia, and MIT.

Come back to Xconomy for my colleague Luke Timmerman’s upcoming interview with Alnylam chief executive John Maraganore about this litigation involving Tekmira. Also, here’s Luke’s previous report about this litigation from earlier this week. Tekmira’s complaint can be downloaded from this page on its website.

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New England’s biotech attorneys must be working overtime, if the week’s headlines are any indication.

—Cambridge, MA-based Alnylam (NASDAQ:ALNY) announced it had settled a long-standing legal dispute over the so-called Tuschl I and Tuschl II patent families. The suit, which involved key players in the field of RNA-interference including Alnylam, Max Planck Society, the University of Massachusetts, and the Whitehead Institute for Biomedical Research, began in June of 2009 and was slated to go to trial this month.

—No sooner did Alnylam wrap up that litigation than it was hit with a huge lawsuit from its Vancouver, BC-based partner Tekmira Pharmaceuticals, which is accusing Alnylam of misappropriation of trade secrets, unfair competition, and more—and is seeking damages of more than $1 billion. The suit centers on technology for delivering RNAi therapeutics—a notorious challenge in the field. For its part, Alnylam called Tekmira’s complaint “without merit or foundation,” and said it intends to defend itself fully.

—Elsewhere in Cambridge, Genzyme (NASDAQ:GENZ) faced a lawsuit as well. It and Mt. Sinai Medical School are being sued by six patients with Fabry disease over the handling of a rationing system for agalsidase beta (Fabrazyme), Genzyme’s treatment for Fabry. Supplies of the drug were short following a temporary closure in 2009 of the company’s Allston, MA, plant.

—In non-legal news, Cambridge based Tolerx and its partner GlaxoSmithKline (NYSE:GSK) reported that otelixizumab, their experimental drug for Type 1 diabetes, failed to meet its main clinical goal in a late-stage study called Defend-1. While the companies are … Next Page »

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[Updated 3/15/11, 2:28 pm ET. See note below] Litigation concerning key patents involved in the development gene-silencing drugs known as RNA-interference therapies has been settled. Cambridge, MA-based Alnylam Pharmaceuticals (NASDAQ:ALNY), a developer of RNAi therapies, said today that the firm and all others involved in the lawsuit over certain rights to the Tuschl I and Tuschl II families of patents have reached an agreement.

The litigation began in June 2009 and was set for trial this month in federal court in Boston. It involved several major players in the field of RNAi—which offers the promise of turning off disease-related genes to treat illnesses such as cancer—including Alnylam, Max Planck Society, the University of Massachusetts, and the Whitehead Institute for Biomedical Research. Now all those groups, including MIT, a former party to the litigation, have reached a deal that clarifies the rights to the key patents.

The groups have agreed to give Germany’s Max Planck, which has for years made Alnylam its exclusive licensee of the Tuschl II patent family, the lead role in coordinating the prosecution of the Tuschl I and Tuschl II family of patents in the U.S. Max Planck is also continuing this lead role in prosecuting the Tuschl II patents in markets outside the U.S. The University of Massachusetts will now lead prosecution of the Tuschl I patents outside of the U.S., and Alnylam has agreed to grant UMass permission to sublicense the U.S. Tuschl II patents to the U.S. drug giant Merck (NYSE:MRK) under certain limitations in return for a portion of sublicensing revenue, according to the firm’s press release.

“It’s good for Alnylam to have it out of the way,” Alan Carr, a biotech analyst for Needham & Company, said this morning. “I think that with Max Planck managing most of the patent prosecution, that is going to be a positive thing” for Alnylam.

Alnylam, which is at various stages of developing RNAi treatments for respiratory syncytial virus, liver cancers, and Huntington’s disease, has always regarded the Tuschl II patent family as important to its intellectual property position. The company, founded in 2002, has no products on the market and has brought in millions of dollars in revenue over the years from licensing and partnership deals with major drugmakers such as Novartis, Roche, and Takeda.

“Today’s settlement provides for a favorable resolution of this dispute for all parties and significantly optimizes the successful prosecution of both the Tuschl I and Tuschl II patent families, which together represent critical innovations for the advancement of RNAi therapeutics as breakthrough medicines,” said John Maraganore, CEO of Alnylam, in a statement.

Barry Greene, Alnylam’s chief operating officer, said in an interview this afternoon that the fact that the settlement gives Max Planck a lead role in prosecuting the U.S. Tuschl I and Tuschl II patent families is a win for Alnylam. “We’ve maintained all along that Alnylam intellectual property was required by all involved in the development and commercialization of RNAi therapeutics,” he said. “Today’s settlement further strengthens that belief.”

My colleague Luke Timmerman interviewed Maraganore in December after Roche’s decision to end its RNAi research programs and Novartis‘s earlier decision not to extend its collaboration with Alnylam, which triggering layoffs of 25-30 percent of Alnylam’s work force in September.

[Commentary from Alnylam COO Barry Greene was added to the original version of this story.]

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This week we’ve seen financings and acquisitions news spanning the life sciences, IT, and cleantech sectors in New England.

—OpenMile, a Boston- and Chicago-based developer of Web and mobile technology for optimizing shipping, said it raised $6 million in a Series B deal led by Globespan Capital Partners, with participation from existing investor Charles River Ventures.

—Waltham, MA-based Bluespec, a maker of software for designing electronics components, grabbed $1 million in equity-based funding from four investors, an SEC filing showed. The company’s previous investors include Atlas Venture and North Bridge Venture Partners.

—DynamicOps, a Burlington, MA-based maker of software for cloud infrastructures and IT virtualization, snapped up an $11.3 million equity-based financing. The company was spun out of Credit Suisse in 2008.

—Marlborough, MA-based CardioFocus brought in $30.6 million to put toward its medical devices, which include a product for treating an irregular heart rhythm known as atrial fibrillation. The money comes from new investors First Alliance & Capital Invest, Fletcher Spaght Ventures, and Manatuck Hill Partners, as well as all of the startup’s previous investors.

—Boston non-profit Diagnostics For All nabbed a $3 million grant from the Bill & Melinda Gates Foundation and the UK’s Department for International Development to fund the creation of three new tests aimed at improving safety and productivity in agriculture. Diagnostics For All first spun out of Harvard to focus on diagnostic products in the human health space, and is led by veteran biotech executive Una Ryan.

—CHiL Semiconductor of Tewksbury, MA, said it is being acquired by Los Angeles-based power management firm International Rectifier (NYSE: IRF) in a $75 million cash deal expected to … Next Page »

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