OncoSec Medical CEO Punit Dhillon tells me the startup he helped establish in San Diego last March is beginning mid-stage safety and efficacy trials of its proprietary technology for enhancing drug delivery in treatments of several types of skin cancer.

The technology, which OncoSec acquired from Blue Bell, PA-based Inovio Pharmaceuticals (AMEX: INO) almost a year ago, transmits intense electrical pulses into skin tumors through six electrode needles that are pushed into the skin. The electricity causes the tumor cells to become permeable with each jolt, and makes it easier for anti-cancer drugs injected into the region to pass through the tumor cells’ tough outer membrane. Known as electroporation, the process increases the concentration of an anti-cancer drug within the tumor.

“What we’re doing is a much more elegant and targeted approach,” says Dhillon, who estimates the technique increases the uptake of anti-cancer drugs by 4,000 to 10,000 times. As a result, doctors can reduce the dosage of anti-cancer drugs used with electroporation technology.

Dhillon, who previously served as Inovio’s vice president of finance and operations, says Inovio has been an electroporation pioneer. The Pennsylvania company decided last year, however, to sell technology that was unrelated to its strategic focus on developing DNA vaccines for cervical dysplasia, leukemia, and hepatitis C virus therapies.

The deal to acquire Inovio’s assets didn’t happen by chance. Inovio chairman and former CEO Avtar Dhillon is Punit Dhillon’s uncle, and their family and friends raised the initial $1.1 million that funded OncoSec after the company sprang to life through a reverse merger with a dormant public company. The San Diego startup raised another $3 million last June from two New York health funds, Hudson Bay Capital and Heights Capital. That should be enough cash for OncoSec to complete three mid-stage trials the company plans to begin before the end of March.

The three studies will use OncoSec’s electroporation technology to deliver the company’s lead drug candidate, called Interleukin-12 (IL-12) cytokine, to three groups of patients with different lethal skin cancers—metastatic melanoma, Merkel cell carcinoma, and cutaneous T-cell lymphoma. The experimental drug is intended to both trigger and boost a strong immune response to each type of cancer. The combined treatment, known as electroimmunotherapy, represents a potential new anti-cancer treatment with broad applicability, although Punit Dhillon says the company must pursue separate regulatory approvals to treat each type of cancer (as a combination drug-and-device product) on an application-by-application basis.

OncoSec says its technology also can be used in the same way in electrochemotherapy, which uses an established anti-cancer drug like bleomycin while a tumor is being electroporated. The use of electroporation in chemotherapy has been studied more throroughly, and Punit Dhillon says he wants to advance OncoSec’s approach through a partnership with a bigger pharmaceutical company.

“2011 was a great year for us,” he says, “and we’ve got some exciting milestones to look forward to in 2012.” Once the latest studies have been completed, OncoSec’s Dhillon says he looks forward to licensing opportunities and other commercial prospects, and he adds, “We also still have the chemotherapy program in the wings.”

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Applied Proteomics hasn’t exactly been operating in stealth mode since it was founded five years ago. Co-founders David Agus, a cancer specialist at USC, and Danny Hillis, the MIT-trained computer scientist, gave TedMed talks about the startup’s technology, which provides a 40-gigabyte snapshot of all the proteins circulating in a drop of blood. By pure coincidence, I watched John Stewart’s Feb. 2 interview with Agus last night on “The Daily Show.”

“Danny and David had the foresight to build the tool before trying to use the tool,” says John Blume, a molecular biologist who joined API in 2008 as chief scientific officer. “Although the company wasn’t in stealth mode, the first several years were spent in taking the time to make it right, and then to use it and avoid some of the stumbling blocks.”

Now Applied Proteomics is raising the curtain on several steps that mark its progress beyond a seed-stage startup that was incubating at Applied Minds, an industrial think tank that Hillis founded in Glendale, CA, with a colleague from Disney Imagineering. After moving the headquarters to San Diego late last year, Applied Proteomics is today naming a new CEO—Peter Klemm, a veteran in molecular diagnostics and the former CEO of Lexington, MA-based Predictive Biosciences.

Danny Hillis

The company known as API says it also secured $22.5 million last June in Series B funding from Domain Associates (San Diego partner Jim Blair joined the board), Seattle’s Vulcan Capital, and returning angel investors. Klemm tells me the company raised $4 million from angel investors (who prefer to go unnamed) in what amounted to API’s Series A round in 2007.

David Agus

API’s goal, Klemm says, is nothing less than to “elevate molecular diagnostics to another level beyond the genome” by measuring the proteins made by genes—a long-sought technology that is expected to help doctors improve medical care for individual patients. Because proteins carry out most cellular functions, the company says a snapshot of all the proteins circulating in the body at a given moment represents “the most powerful source of information” in terms of understanding a patient’s health status.

Quantifying all the proteins in the body, Klemm says, can help doctors optimize the course of treatment for individual patients by making it easier to identify the specific drugs that would have the greatest effect on blocking specific proteins or signaling pathways, which can vary dramatically from person to person.

In a statement from the company, Hillis says, “For the first time, we can look at all the proteins in the body with remarkable specificity and sensitivity and use proteomic technology to create … Next Page »

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Seattle-based Dendreon Corp. (NASDAQ: DNDN) said today it has named John Johnson to the position of president and CEO, succeeding longtime CEO Mitchell Gold. Johnson was previously the CEO of East Brunswick, NJ-based Savient Pharmaceuticals (NASDAQ: SVNT).

The appointment comes after a difficult run for Dendreon. In 2010, the company won approval for sipuleucel-T (Provenge), the first in a new class of immune-boosting therapies for prostate cancer. But the product has been slow to take off, causing the company to fall short of Wall Street expectations. On January 5, Dendreon surprised investors by announcing that it sold $228 million of the drug in 2011—better-than-expected results—but it hasn’t been enough to sway shareholder sentiment.

Today’s news was welcome on Wall Street. “I am very pleased to hear this morning about Dendreon’s succession plan for its CEO and Chairman,” wrote shareholder activist Brad Loncar in a statement.” In August, Loncar sent a letter to Dendreon chairman Richard Brewer expressing concerns about poor management at the company. “After joining together and asking for this change, this is a big win for Dendreon’s shareholders and for corporate governance in general.”

Dendreon’s shares rose 6 percent to $14.40 in pre-market trading.

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Cell Therapeutics suffered an embarrassing defeat the last time it appeared in front of an FDA advisory panel and today the company made a move that will enable it to avoid another public shellacking, at least for a while.

The Seattle-based biotech company (NASDAQ: CTIC) said today it has withdrawn its application to start selling pixantrone (Pixuvri) as a new lymphoma drug in the U.S. after saying today it needed more time to prepare for a Feb. 9 meeting of the FDA’s cancer drug advisory panel. The company said it asked the FDA to allow it to present at the March meeting instead, but when the agency said no, Cell Therapeutics withdrew the application. That means the agency’s April 24 deadline to complete its review of the application has been voided, although Cell Therapeutics said today it plans to resubmit its application later in 2012.

The last time Cell Therapeutics appeared at the FDA’s Oncologic Drugs Advisory Committee (ODAC), in March 2010, the panel voted 9 to 0 against the company’s pixantrone application. The chair of the FDA panel at the time, Gail Eckhardt of the University of Colorado at Denver, said the Cell Therapeutics application was “disturbing,” partly because it only enrolled 140 of the 320 patients needed to generate a statistically valid result. The head of the FDA’s cancer drug office, Richard Pazdur, said at the time that the Cell Therapeutics application depended on “a single incomplete trial.” The initial application was turned down by the FDA in April 2010.

By withdrawing the application just before the next advisory panel, Cell Therapeutics contradicted one of its own statements from less than a month ago, when it said it believed it had addressed the concerns raised by the FDA.

“We are pleased the Office of Oncology Drug Products (OODP) chose to bring our pixantrone new drug application back to ODAC for review now that we have provided additional information and data recommended by the Office of New Drugs (OND) that we believe addresses the issues raised in the OODP Complete Response Letter of April 2010,” James Bianco, the company’s CEO, said in a Jan. 3 statement.

Shares of Cell Therapeutics fell 18 percent today to $1.09 in early trading.

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Bad news out today from Infinity Pharmaceuticals. The Cambridge, MA-based biotech company said it is halting a mid-stage clinical trial of its drug for pancreatic cancer early after learning that patients were living longer in the placebo comparison group. Infinity (NASDAQ: INFI) shares fell more than 30 percent after the news.

The trial of 122 patients showed that when patients got Infinity’s saridegib (IPI-926) in addition to gemcitabine chemotherapy, they were living less than the six months they were expected to based on historical studies with the chemo drug alone. No unexpected side effects were seen among patients on the Infinity drug or in the control group, the company said.

This is a painful setback for Infinity. The company just last week released some more encouraging data from an early-phase study of the drug in 16 patients, which suggested it offered a benefit by shrinking tumors and helping them live a median time of about 10 months. The plan for this year was to wait for the results from the more rigorous study of 122 patients, to get a firm answer on whether it could help pancreatic cancer patients live more than the expected six months. Even though the drug failed in that study, Infinity said it still believes in the drug’s potential because it inhibits a pathway known as hedgehog that plays a role in multiple cancers. Infinity currently is testing the new compound in mid-stage trials against myelofibrosis and chondrosarcoma. Those studies are continuing, the company said.

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Prostate cancer was once a backwater for innovation, but suddenly it’s become one of the most competitive battlegrounds in all of biotech. And one of the darkhorses in this race, Bothell, WA and Vancouver, BC-based OncoGenex Pharmaceuticals, is getting ready to show next week whether it has another contender in the pipeline.

OncoGenex (NASDAQ: OGXI) is preparing to release interim results next week from a clinical trial that could offer a hint of effectiveness of a prostate cancer drug called OGX-427. If OncoGenex can show in this 72-patient study that its compound is slowing the spread of tumors, and lowering prostate-specific antigen (PSA) scores, then it could be in position to run a more meaningful trial that asks whether it can prolong lives, or work well in combination with other therapies. The preliminary data are expected Feb. 2 at the American Society of Clinical Oncology’s Genitourinary Cancers Symposium in San Francisco.

Results from this trial, and another study among patients with bladder cancer, mean a lot for OncoGenex during what has been a long period without much big news for investors and researchers to chew on. The company is now enrolling 800 patients into a pivotal study of its lead prostate cancer drug, custersin, but expects it will have to wait until the fourth quarter of 2013 to find out whether that treatment can extend lives of prostate cancer patients. While OncoGenex makes that long slog through development, it has seen companies like Dendreon, Johnson & Johnson, Medivation, Bayer, and Exelixis continue to jockey for position at various stages of therapy, each with distinct modes of treatment, for men with prostate cancer. The disease kills about 30,000 men in the U.S. each year.

“A lot of focus for us is on custersin, but while that’s going on, we continue to mature our OGX-427 data,” Michelle Burris, OncoGenex’s executive vice president of operations, said during a meeting at the JP Morgan Healthcare Conference earlier this month. While she notes the second OncoGenex drug has shown encouraging ability to work on its own in small studies, she acknowledged it will have to find a niche in a competitive landscape—and says that it can. “It plays nice with a number of different therapies,” she says.

Michelle Burris, OncoGenex's executive vice president of operations

The OncoGenex drug, given through an IV infusion, is designed to work by blocking a biological target known as heat-shock protein 27 (Hsp27). That protein is believed to play a role in helping cells survive under stressful conditions. It’s supposed to help stabilize proteins that keep cells from committing suicide. By inhibiting its activity, you could in theory allow cancer cells to naturally undergo the cell death (apoptosis) process. But there’s also another mechanism of hsp27 that researchers find interesting. It is thought to work as a “chaperone” molecule that helps shuttle in male hormones that fuel prostate tumors.

Researchers believe that could be useful because hormone deprivation therapies have long been standard treatment for prostate cancer, and patients end up developing resistance over time. Two new hormone-blocking therapies, Johnson & Johnson’s abiraterone (Zytiga) and Medivation’s MDV-3100, have both been shown in clinical trials to extend lives of men who resist conventional treatments by blocking male androgen receptors in a different way. OncoGenex’s bet is that even while those drugs are doing their thing, Hsp27 is operating as a chaperone that allows some residual androgens into the tumor, which help provide it with some sustenance.

This theory of cancer biology is being tested in a trial sponsored by the British Columbia Cancer Agency, and led by Kim Chi. The key study enrolled 72 patients with prostate cancer that … Next Page »

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It was a busy news week in the New England life sciences scene, with acquisitions, clinical data, and partnership deals.

—Thanks to a new co-promotion deal, Genzyme will begin marketing a diagnostic test for thyroid cancer developed by South San Francisco-based Veracyte. Genzyme, the Cambridge, MA-based unit of Sanofi (NYSE: SNY) makes a common drug for treating the disease.

—Cambridge-based Infinity Pharmaceuticals (NASDAQ: INFI) presented data from a 16-patient study indicating saridegib, its experimental once-daily pill, could potentially shrink tumors and help people live longer when combined with chemotherapy.

—Millennium, also of Cambridge, nabbed FDA clearance to begin selling a version of the multiple myeloma drug bortezomib (Velcade) that can be injected just under the skin, as well as intravenously. It’s significant because the under-the-skin drug seems to be more tolerable, reducing the drug’s side effect of nerve damage in the fingers and toes.

—Xconomy national biotech editor Luke Timmerman wrote about how Cambridge-based Vertex Pharmaceuticals (NASDAQ: VRTX) and its South San Francisco-based partner Alios Biopharma are positioning themselves to defend their share of the hot growing market for hepatitis C treatments.

—And my colleague Arlene wrote about the family-run business that is Woburn, MA-based Courtagen Life Sciences. Three brothers fill the roles of CEO, president, and chief scientific officer, while their dad chairs the board. Read about more about how it all came together.

—Bedford, MA-based Avila Therapeutics, a maker of so-called covalent drugs for treating cancer, was bought by New Jersey-based Celgene (NASDAQ: CELG) for $350 million upfront. Potentially $575 million more could come to Avila through milestones. The startup’s venture investors included Polaris Venture Partners, Atlas Venture, Abingworth Management, and Advent Venture Partners. Check out investors’ and friends’ reactions to the deal across the Web here.

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Cambridge, MA-based Verastem, the biotech startup seeking to make drugs against cancer stem cells, found a way to rustle up enough demand from investors to complete its initial public offering.

The company (NASDAQ: VSTM) said tonight that it raised $55 million by selling 5.5 million new shares at $10 apiece. It was a strong showing of investor interest, given that Verastem had previously proposed selling just 4.5 million shares, at a range of $9 to $11 a share. UBS and Leerink Swann led the offering, and were assisted by Lazard Capital Markets, Oppenheimer & Co., and Rodman & Renshaw, according to a statement on Verastem’s website. The offering could end up raising more money in the end, because the underwriters have a 30-day option to buy another 825,000 shares. Shares of Verastem will now start trading on the NASDAQ on Friday, the company said in a statement.

The IPO was a bold move in a market that has shown limited interest in such offerings from biotech startups, especially companies like Verastem, which was founded in August 2010 and doesn’t yet have any drug candidates in clinical trials. While Verastem contends that cancer stem cells—also known as tumor-initiating cells—are critical players that help tumors resist treatment and spread, scientists still have a lot to prove about the role they play. The bet here is essentially on an intriguing field of science and a high-profile cast of scientific advisors and executives led by CEO Christoph Westphal. He’s best known as the former CEO of Sirtris Pharmaceuticals, the developer of drugs for diseases of aging, which was sold to GlaxoSmithKline for $720 million in 2008.

Christoph Westphal is chairman and CEO of Verastem

Investors haven’t shown much interest in backing such high-risk/high-reward companies like Sirtris or Verastem lately. Last year, just 10 biotech companies went public, according to a tally from FierceBiotech, down from 13 a year before. At least a couple of other notable biotech companies are teed up to test the IPO market in the early days of 2012—Mountain View, CA-based ChemoCentryx, which is trying to sell 4 million shares at $14 to $16 a share, and Cambridge, MA-based Merrimack Pharmaceuticals, which is attempting to sell 16.7 million shares at $8 to $10 apiece, according to the most recent regulatory filings.

The Verastem offering stands to benefit a number of well-known players in the Boston biotech community. Heading into this deal, the biggest holders in Verastem were Longwood Founders Fund, with a 15.4 percent stake; CHP of Princeton, NJ with 13.5 percent; MPM Bioventures with 13.1 percent; Bessemer Venture Partners with 12.9 percent; Eastern Capital Limited with 7.8 percent; and Advanced Technology Ventures with 5 percent.

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The unsolicited $5.7 billion offer that Roche made for Illumina will no doubt dominate San Diego’s biotech news for weeks to come. We have it and more.

—Switzerland’s Roche offered $5.7 billion, or $44.50 a share, for San Diego-based Illumina (NASDAQ: ILMN in a hostile bid disclosed yesterday. Roche’s bid to stake a claim in genetic diagnostics by acquiring the market-leading maker of DNA sequencing instruments would be the Swiss pharma giant’s biggest deal since its $46.8 billion buyout of Genentech almost two years ago. Roche is the world’s biggest maker of cancer drugs, which suggests its quest for Illumina represents a significant move to base cancer treatments on each patient’s genome.

—Venture capital investors sank $4.73 billion into 446 biotechs nationwide in 2011, according to the MoneyTree report from the National Venture Capital Association, PwC, and Thomson Reuters. But as Luke pointed out in his BioBeat column, there is an alarming drop in support for early stage life sciences startups. Only 153 biotech and medical device startups got their first round of financing in 2011, the lowest amount of seed investment activity in 15 years.

—At an Xconomy dinner discussion, former Amira Pharmaceuticals CEO Bob Baltera said insufficient access to capital is the biggest driver for decision-makers on both sides of biotech-pharma partnerships. So what are some other key factors? We asked some of San Diego’s life sciences leaders to explore the question in an “on the record” dinner discussion late last year.

—San Diego’s Sequenom (NASDAQ: SQNM) completed its secondary public offering, raising roughly $62 million in gross proceeds (before underwriting costs) in the sale of 14.95 million shares, including additional allotments granted to underwriters. Sequenom said it plans to use the net proceeds for … Next Page »

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Millennium is the house that Velcade built, and today it’s gotten the green light to start marketing what it considers to be a new and improved version of the hit drug for multiple myeloma.

The Cambridge, MA-based cancer drug developer, part of Japan-based Takeda Pharmaceuticals, said today it has gotten clearance from the FDA to start marketing a version of bortezomib (Velcade) that can be injected just under the skin, in addition to the usual form given intravenously. Today’s approval means the subcutaneous form of Velcade can be used in every setting where the existing drug is prescribed, for patients with multiple myeloma and mantle cell lymphoma.

While this would ordinarily be considered an incremental advance by providing patients and physicians with a more convenient option, the new Velcade approval could be more meaningful. That’s because the new subcutaneous form of the drug appears to be more tolerable, causing fewer cases of nerve damage in the fingers and toes, which is the most common severe side effect of the existing product. One of the key trials Millennium submitted to the FDA showed it could reduce the rate of moderate to severe peripheral neuropathy from 16 percent to 6 percent by putting patients on the new subcutaneous form. By offering a version that’s equally effective, yet more convenient and tolerable, Millennium is hoping to neutralize one of the advantages that South San Francisco-based Onyx Pharmaceuticals (NASDAQ: ONXX) is playing up for its competing proteosome inhibitor, carfilzomib, that’s being reviewed by the FDA.

“Considering this new subcutaneous route of administration for Velcade is important for our patients, including those with poor vein access and those with pre-existing peripheral neuropathy or a high risk of developing peripheral neuropathy,” said Noopur Raje, director of the Center for Multiple Myeloma at Massachusetts General Hospital Cancer Center, in a Millennium statement. “It’s important to have a range of treatment options to provide the best possible care to each individual patient.”

The Millennium drug was approved by the FDA in 2003. It generated $1.4 billion in worldwide sales in 2009, and is on pace to eclipse $3 billion by 2015, according to BCC Research. About 20,000 people are diagnosed with myeloma each year in the U.S., and 10,000 die from it annually, according to the American Cancer Society. For more background on how the new version of Velcade could change the multiple myeloma landscape, see the FDA approval preview story I ran here last Friday.

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Mark Twain used to toss around a saying about three kinds of lies. There are lies, damned lies, and statistics. This week in biotech, we saw some statistics that could lead some people to get a false impression that everything is just peachy in biotechland.

If you measure the state of life science innovation by the amount of money flowing in, things look swell. Venture capitalists poured $4.73 billion into 446 biotech companies last year, according to the MoneyTree report by the National Venture Capital Association and PricewaterhouseCoopers, based on data from Thomson Reuters. The venture industry association’s press release cheerily noted that overall venture funding jumped 22 percent last year. While software is still the No. 1 and faster-growing sector of the two, biotech held its own, with a solid 22 percent gain in dollars invested compared with a year earlier.

You have to dig deeper to see what’s really going on. There is still a good amount of money going toward late-stage development of drugs people started working on 10-15 years ago. But there is an alarming drop in support for today’s cutting-edge biotech startups. Last year, just 153 U.S. biotech and medical device startups got their first round of financing, the lowest amount of seed investment activity in 15 years, as reported by Ryan Flinn of Bloomberg News.

There’s something really wrong with this picture. Most any biologist will tell you we are living in a golden age of discovery, at a time when we will soon be sequencing entire human genomes for $1,000 in one day. We are able to ask questions about how life works that nobody could even imagine asking a few years ago. It ought to be the time to charge ahead with basic research, and early-stage R&D to test exciting new concepts in diseases like cancer, diabetes, Alzheimer’s, HIV, and more.

But everywhere you look, the story is about cuts, cuts, cuts. The National Institutes of Health, the primary government agency that supports basic biomedical research, used to write checks for one out of every three grant applications, but it’s now down to about one out of every six, NIH director Francis Collins said earlier this month at the JP Morgan Healthcare Conference. Pharma companies are cutting back on R&D, firing workers left and right, and leaning on cheaper outsourced vendors everywhere they can. As many as one-fourth to one-half of biotech venture capitalists are thought to be slowly going out of business, as they are unable to raise new investment funds. The same IPO investors that want to buy Facebook shares look at biotech stocks like a four-year-old looks at lima beans.

There are good reasons why we see all those things happening. Pharma companies have created enormous inefficiencies for themselves through mega-mergers, and now they need to spend years trying to get their houses in order. Biotech as an industry has overpromised and underdelivered, and many investors are tired of it. The FDA, stung by various drug safety scandals, has been cautious about approving new drugs (although there are signs that FDA leadership wants a more balanced approach). And of course, our society is still struggling to come to terms with healthcare reform, and the realization that it’s unsustainable to spend infinite amounts of money on healthcare.

John LaMattina

All that said, an entrepreneur or a bold Big Pharma executive is the kind of person who looks at that picture and believes he or she can overcome the hurdles, and form a plan to turn vision into reality. But there aren’t that many people out there with the can-do spirit, or guts, to put down real money behind really talented teams devoted to the discovery of new drugs. And because everybody’s talking about how to go from Phase I to Phase II with drugs people invented years ago, there’s a real possibility that once those projects run their course, we’ll all look around in 2020 and wonder where all the wonderful new drugs are going to come from.

“You can really get into a vicious cycle when you have to eat your own seed corn,” says John LaMattina, a senior partner with PureTech Ventures, and the former president of R&D at Pfizer.

There are exceptions, of course, with a few people trying creative new ways to plant seed corn. Third Rock Ventures and Atlas Venture are a couple of VC firms that have remained active, continuing to bet big on the edgiest stuff coming out of the labs. Most every Big Pharma company has set aside cash for corporate venture firms that are seeking to help fill the void being created by the shrinkage of traditional VC. Pfizer, Johnson & Johnson, Sanofi, Bayer, and deserve credit for working on creative new collaborations with top biomedical universities and research centers, which seek to minimize some of the problems with the fruitless alliances of the past. J&J made news this past week when it unveiled an incubator for 18-20 startups in San Diego which looks to fill up some lab space it had vacated through its own internal R&D cutbacks.

Right now, we are in an age of experimentation with new organizational structures for supporting biomedical R&D. The hope is that these new organizations can reduce the time, money, and high-risk profile that has made life sciences such a hit-or-miss investment over the years. Pharma companies know they don’t … Next Page »

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Infinity Pharmaceuticals released some preliminary data last June that suggested it may be onto something for pancreatic cancer, and now it has gathered a bit more evidence to support its case.

The Cambridge, MA-based biotech company (NASDAQ: INFI) is announcing results today from a small study of 16 patients that suggest its experimental once-a-day pill, saridegib (IPI-926), may be able to shrink tumors and help people live longer when given in combination with chemotherapy.

The data is still from a small sample, so it will need to be confirmed in more patients before it be considered convincing. As reported back in June, five of the 16 patients (31 percent) had significant tumor shrinkage. Now with more follow-up time, researchers are reporting that the tumors were kept from spreading for a median of 7.6 months, and the patients lived a median time of 10.2 months, according to data being presented at the American Society of Clinical Oncology’s Gastrointestinal Cancers Symposium in San Francisco. There was no way to compare how good this performance was since there was no control group in the trial, but historical studies have shown patients with this diagnosis can expect to live about six months.

Infinity is betting big that it can confirm the results from this small study, in an ongoing trial of 120 patients, which will randomly assign patients to the new drug or a control group, and measure how long each group of patients lives. Once enough patients have died to get a good statistical comparison between the two groups, Infinity will unblind the data and release it. That eagerly awaited result is expected in the second half of 2012.

Infinity Pharmaceuticals CEO Adelene Perkins and R&D head Julian Adams

“We’re definitely in the game,” said Julian Adams, Infinity’s president of R&D, in an interview last week at the JP Morgan Healthcare Conference in San Francisco. “If the next trial performs like this one, we will have very significantly changed the landscape for pancreatic cancer.”

Many biotech companies have tried, and failed, to make much difference for pancreatic cancer, which often isn’t diagnosed until it has already spread through the body. About 36,800 people in the U.S. die each year from pancreatic cancer, according to the American Cancer Society.

The trial of this drug (pronounced “suh-RID-uh-gib”) will carry a lot of meaning for both physicians and cancer biologists. That’s because the compound is designed to inhibit a biological target known as Smoothened, a component of the Hedgehog pathway that is thought to help tumors grow and thrive when it’s turned into a mutated form. Infinity scientists showed, in a paper published in Science in 2009, that the drug disrupted the dense tissue matrix that encases tumors, Adams says. By altering the tumor’s microenvironment, the Infinity drug is thought to break down the tumor’s “cement-like fibrotic shell” and allow chemotherapy to get inside where it can kill cancer cells.

The drug’s mechanism means that it wouldn’t be used as single treatment on its own, but rather in combination with chemotherapy, Adams says.

Side effects of the drug appeared to be pretty typical for cancer trials. Of the 16 patients in this study, seven got the highest dose, 160 milligrams, which was selected for the ongoing trial of 120 patients. At that dose, two of the seven patients had moderate to severe depletion of their infection-fighting white blood cells, one had moderate to severe anemia, and another case was reported of elevated liver enzymes, which can be a sign of liver damage. No patient deaths were attributed to the Infinity drug or the chemo agent, researchers said.

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Veracyte has been gaining momentum the past few months with a new molecular diagnostic for thyroid cancer, and today it’s taking another step ahead by forming an alliance with Genzyme, the maker of a common drug for treating the disease.

South San Francisco-based Veracyte said today that it has formed a global co-promotion deal with Genzyme, the Cambridge, MA-based unit of Sanofi, in which the bigger company will start marketing Veracyte’s Afirma test. Financial terms of the deal aren’t being disclosed.

Veracyte, which was featured here in November, has been selling a gene expression test over the past year to help doctors determine when a lump in the thyroid gland is benign, or potentially malignant. Almost 500,000 suspicious thyroid lumps get biopsied in pathology labs every year, and about 20 to 30 percent of those tests offer “inconclusive” results. Fearing the worst, many of those patients go on to have surgery to remove their thyroid glands at a cost of about $12,000 to $16,000 apiece, plus a lifetime of thyroid hormone medications.

Veracyte’s proposition to doctors is that by doing a standard fine-needle biopsy test, and paying $3,500 for Veracyte to perform its Afirma gene expression analysis, they can rule out malignancies early in the game. That is supposed to cut down on unnecessary surgeries, and save insurers some money. Earlier this month, a Medicare contractor that covers 40 million people said it has agreed to cover the test.

Genzyme has long had interest in the thyroid cancer field, through its marketing of thyrotropin alfa (Thyrogen). “Together, our products offer patients and physicians a powerful personalized medicine solution for the diagnosis and treatment of thyroid cancer, addressing an unmet need in the community and improving patient outcomes,” said Genzyme’s head of rare diseases, Rogerio Vivaldi, in a statement.

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The drug that made Millennium into a biotech power is on the verge of getting a subtle but meaningful upgrade, just in time to help the company fend off a serious new competing therapy from South San Francisco-based Onyx Pharmaceuticals (NASDAQ: ONXX).

Cambridge, MA-based Millennium, the cancer drug unit of Takeda Pharmaceuticals, is awaiting word from the Food and Drug Administration on whether it can start marketing a new version of bortezomib (Velcade) that can be injected just underneath the skin. The U.S. drug regulatory agency has a deadline of Jan. 23 to complete its review of Millennium’s application for the subcutaneous form of the treatment, which would be a new option beyond the current version that’s given intravenously.

Ordinarily, this kind of application would be an incremental advance. But the FDA’s decision could mean a lot to Millennium, because the new subcutaneous form is not only faster and more convenient for hospitals to administer, but clinical trials show it causes less nerve damage in the fingers and toes than the conventional IV product. If the FDA agrees to allow Millennium to market the new version, then Millennium will have a stronger defense against emerging competition from Onyx Pharmaceuticals, which is angling for FDA clearance of a rival drug that has long claimed to have an advantage with its milder side effects.

The Millennium drug, approved by the FDA in 2003, generated $1.4 billion in worldwide sales in 2009, and is on pace to eclipse $3 billion by 2015, according to BCC Research. About 20,000 people are diagnosed with myeloma each year in the U.S., and 10,000 die from it annually, according to the American Cancer Society.

“There are all kinds of ramifications that will make this quite an attractive option for patients,” Deborah Dunsire, the CEO of Millennium, said last week in an interview at the JP Morgan Healthcare Conference in San Francisco.

The whole idea of packaging Velcade in a new way wasn’t something that came from Millennium scientists, and they didn’t expect it would make much difference. The idea for developing a subcutaneous form came after a nurse in France improvised when it was too difficult to find a vein in an elderly patient, Dunsire says. It turned out the patient did well on this improvised injection, and the doctor decided to try to study the new injection mode further, she says.

When Millennium got wind of some promising early results, it designed a study of 222 patients to compare those on standard Velcade with patients on the new subcutaneous version, to see if they were roughly the same. A subcutaneous version, after all, has a natural convenience advantage in that patients don’t have to … Next Page »

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Bayer and Onyx Pharmaceuticals looked like they hit gold last fall, when a study of 760 patients showed that one of their new cancer drugs was able to help patients with colorectal cancer live longer.

Today, researchers got the first glimpse at the detailed results, and while it’s encouraging news for the companies and for patients, it’s not exactly something to shout about from the rooftops.

The new drug from Bayer and South San Francisco-based Onyx (NASDAQ: ONXX) showed that it helped patients live a median time of 6.4 months with colorectal cancer that had spread through the body, compared with a median of five months for those in the placebo group. The new drug, regorafenib, had significant side effects like almost all cancer drugs. About 17 percent of patients had moderate to severe skin reactions on their hands and feet, while 15 percent had significant fatigue, and 8 percent had significant diarrhea, researchers said today at the American Society of Clinical Oncology’s gastrointestinal cancer symposium in San Francisco. There was nothing new or unexpected in the drug’s safety profile, scientists said.

Onyx and Bayer have long worked together to co-market sorafenib (Nexavar) as a treatment for kidney and liver cancers, but the relationship was frayed recently by litigation over who owns the second, related compound. The companies settled that dispute in October, in an arrangement where Onyx got a $160 million one-time payment and will get a 20 percent royalty on worldwide sales of the new drug. That royalty stream suddenly looked valuable two weeks later when an independent monitoring committee looked at the data of the ongoing study known as Correct, saw the survival edge, and recommended the study be halted earlier than planned so all patients could get the experimental medicine.

Onyx Pharmaceuticals CEO Tony Coles

Analysts are now projecting regorafenib will be a billion-dollar seller, which could throw off hundreds of millions in annual revenue to Onyx. If the drug wins regulatory approval, it could offer colorectal cancer patients a new option beyond existing drugs like Eli Lilly’s cetuximab (Erbitux), Roche’s bevacizumab (Avastin), and Amgen’s panitumumab (Vectibix). About 52,000 patients in the U.S. are expected to die this year from colorectal cancer, according to the American Cancer Society.

“We’ve shown an improvement in overall survival, which we think is really terrific because these are third and fourth-line metastatic patients who have gone through almost all other available options,” Onyx CEO Tony Coles said in an interview last week at the JP Morgan Healthcare Conference, before the details were released.

Bayer said in a statement today that it plans to seek regulatory approval later this year for clearance to start selling the drug for patients with colorectal cancer that has spread.

Colorectal cancer isn’t the only place where Bayer and Onyx see the new drug potentially being used. The companies are expecting to see results from a pivotal study of 350 patients with gastrointestinal stromal tumors (GIST) before the end of March, Coles says. “Between the colorectal cancer data, and the GIST data to come, regorafenib is clearly on the scene,” Coles says. “The two companies are working together to pursue other indications.”

Few analysts last fall were counting on any revenue at all from regorafenib, so it was a surprising and transforming piece of news for the company. As Coles put it, “we are in position to go from one product for two tumors (Nexavar) to potentially three products with strong data or [an FDA clearance] for seven different cancers by the end of this year,” Coles says. The other drug besides Nexavar and regorafenib is known as carfilzomib, which is being reviewed by the FDA as a new treatment for multiple myeloma.

“When you see that kind of momentum in the business in such a short period of time, it’s unrivaled,” Coles says. “We think the future is very bright.”

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Seattle Genetics is getting some new warnings, including one new language about a potentially deadly brain infection, put into the FDA-approved prescribing information of its lone marketed product.

The company (NASDAQ: SGEN) said today it is working on an update to the label for brentuximab vedotin (Adcetris), which will include a boxed warning about the risk of patients on the lymphoma drug getting a potentially fatal brain infection called progressive multifocal leukoencephalopathy (PML). Seattle Genetics’ original drug label, cleared by the FDA in August, said there had been a case of PML in clinical trials, but now that the drug has been used more widely on the market, Seattle Genetics discovered a second case last fall, and said today it has learned of a suspected third case of PML. That information is prompting new warning language that’s supposed to help doctors spot signs of PML.

Several new biotech drugs have been linked to cases of PML, including Roche and Biogen Idec’s hit lymphoma drug rituximab (Rituxan). The Seattle Genetics drug is designed to hit a different target on cancer cells, and it is approved for use in a couple of rare malignancies—Hodgkin’s disease and anaplastic large cell lymphoma. The new treatment has shown strong ability to shrink tumors in clinical trials in the majority of patients who have essentially run out of options, and it has beaten Wall Street’s initial sales expectations. Now Seattle Genetics is looking to expand use of the drug to larger groups of patients. One of those label-expansion studies showed that the new drug shouldn’t be used in combination with a chemotherapy agent known as bleomycin, because of an elevated rate of lung toxicity, so a warning about that is also being incorporated into the Adcetris label.

The bleomycin warning isn’t much of a concern, because even though it’s part of a typical chemo regimen, Adcetris was never approved to be used in combination with that drug, and researchers are hopeful that Adcetris might be able to replace bleomycin for use in some patients, because the new drug has a milder side effect profile when used on its own.

“Our first priority is patient safety. By developing these agreed upon label updates with the FDA regarding PML and the contraindication with bleomycin, we aim to heighten awareness among healthcare professionals in order to most safely treat their patients with Adcetris. Although PML in lymphoma patients can be caused by factors such as underlying disease and prior therapies that affect the immune system, a contributory role of Adcetris cannot be excluded,” said Tom Reynolds, the chief medical officer of Seattle Genetics, in a statement.

Previous studies have said patients with blood cancers have about a 0.07 percent chance (1 in 1,400) of getting PML. Seattle Genetics didn’t say what the ratio is for patients getting Adcetris, but it has had two confirmed cases, and one suspected case, out of more than 2,000 patients worldwide who have gotten the new drug.

Shares of Seattle Genetics fell about 6.3 percent to $17.28 at 10:14 am Eastern time.

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There was a whole lot of life sciences news over the past week. Here’s my roundup.

—Carlsbad-based Life Technologies (NASDAQ: LIFE) said it’s taking orders for a benchtop genome sequencer that can to decode an individual’s DNA within 24 hours and at a cost of roughly $1,000. The company priced its new Ion Proton Sequencer at $100,000 to $150,000, which also represents a dramatic reduction compared with the cost of existing DNA sequencers, and might even entice some practicing physicians to buy into the idea of personalized medicine. A cross-town rival, San Diego-based Illumina, also introduced an improved version of its gene-sequencing machine capable of same-day service, although Forbes’ Matthew Herper says Illumina’s HiSeq 2500 is priced at $740,000.

—A $1 million gift to the Tech Coast Angels from the family of slain TCA member and life sciences investor John G. Watson has enabled the angel group to establish a nonprofit foundation to support entrepreneurism in the San Diego region. A financial adviser, who awaits sentencing following his conviction two months ago, murdered Watson in his La Jolla town home. Watson’s sister, Gillian Ison, told the TCA, “John loved investing, innovation, and the entrepreneurial spirit that he discovered when he arrived in San Diego. We believe that a foundation supporting entrepreneurism is the best way to honor his memory and his life.”

—San Diego’s AnaptysBio said it has established strategic alliances with Novartis and an undisclosed pharmaceutical company. The company plans to use its proprietary technology to discover and develop new therapeutic antibodies with multiple cancer-related therapeutic targets. AnaptysBio said the two deals provide global rights to develop and commercialize a limited number of antibodies against each cancer target that AnaptysBio generates.

—In his BioBeat column, Luke previewed the five myths likely to make the rounds at this week’s JP Morgan Healthcare Conference in San Francisco. You could say that Luke inoculated readers from excessive optimism by writing, “Hope and hype are a couple essential ingredients in this business, and every year both are on display at this conference. Sometimes the wishful thinking can congeal into conventional wisdom.” Is that good, or what?

— Wylie Vale, a Salk Institute scientist, renowned expert on brain hormones, and founder of San Diego’s Neurocrine Biosciences (NASDAQ: NBIX), died on Jan. 3 while vacationing in … Next Page »

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Forma Therapeutics has the hot hand among biotech startups in the early days of 2012. Today, it is announcing it has struck its second alliance with a Big Pharma company that wants Forma’s help discovering cancer drugs.

The Watertown, MA-based biotech company is announcing today that Janssen Biotech, a unit of New Brunswick, NJ-based Johnson & Johnson (NYSE: JNJ) has agreed to collaborate with Forma to find drugs that can throw a wrench into the overactive metabolic pathways of cancer cells. Forma isn’t disclosing how much upfront or ongoing research support it will get from Janssen, but did say it could get as much as $700 million over the years in development, regulatory, and commercial milestone payments if the discovery effort generates real drugs.

The new alliance comes less than a week after Forma struck a partnership with Germany-based Boehringer Ingelheim, which agreed to pay Forma $65 million over the next four years, plus milestones, to discover cancer drugs against certain hard molecular targets known as protein/protein interactions. The latest deal means that Forma has now secured four partnerships in the past 14 months, with large organizations throwing their support behind Forma’s 100-person drug discovery crew. Taken together, those deals have provided Forma with $175 million of upfront cash and research support over the next four years, and made the startup eligible for up to $2.5 billion in milestone payments. Even if none of the big milestone checks arrive, the upfront and research support has enabled Forma to build a discovery team with enough capability to rival what some Big Pharma companies devote to the earliest stages of cancer R&D, CEO Steve Tregay has said.

“It’s been a good 14 months for us,” Tregay says.

Steven Tregay

The field of cancer metabolism, in which researchers seek to fight tumors by essentially starving them of essential nutrients, has become one of the hot niches in cancer biology. Cambridge, MA-based Agios Pharmaceuticals has staked out a position as an early leader in the field, with backing from Summit, NJ-based Celgene (NASDAQ: CELG). This also isn’t the first deal Forma has done in the field—it agreed back in June with South San Francisco-based Genentech to collaborate on a program to develop a drug that fights the overactive metabolism of cancer cells. That deal also had an unusual twist, in which Forma agreed that if Genentech exercises an option to acquire full rights to a new drug candidate, then Forma will be able to deliver the proceeds as returns to its investors—without getting acquired or attempting to go public.

This latest transaction with Janssen Biotech has its own twist. Forma’s strength is mainly in the early-stage discovery, but in this case it has retained the potentially lucrative opportunity to co-develop and keep North American product rights to one of the drugs it discovers. And the two parties both have the option to expand the drug discovery effort beyond the realm of cancer cell metabolism.

Holding onto North American product rights is a key part of Forma’s strategy to evolve over time from a pure discovery-based organization into more of a diversified operation that does early and late-stage R&D. And there could be a lot more money for Forma and its shareholders if even one of the many molecules it discovers turns out to be a big hit for cancer. Keeping some North American commercial rights “is a key element of our strategy to create long-term shareholder value,” Tregay said in a statement.

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Some people set a goal of losing weight in the new year, but if you’re Bob Langer and Omid Farokhzad, it’s apparently time to start another new biotech company.

The prolific biotech entrepreneurs (Langer is from MIT, while Farokhzad is at Harvard Medical School), along with colleague Stephen Lippard of MIT, said today they have come together to start another new company called Blend Therapeutics in Watertown, MA. Langer and Farokhzad, who previously put their heads together for Bind Biosciences and Selecta Biosciences, now hope to come up with novel combinations of medicines that they say should “target distinct disease pathways with optimal efficacy and safety.” Flagship Ventures, New Enterprise Associates, and NanoDimension have invested $2.8 million to start Blend, according to a report in FierceBiotech.

The company plans to hire about a dozen people this year, and will grow “methodically” until it is mature enough to hire a top-tier CEO, FierceBiotech said. Farokhzad told the industry news site that Blend could have raised more money, but opted instead to raise a smaller sum, create some value, and then raise more money. The initial plan, Farokhzad said, is to focus on treatments for cancer, inflammation, pain, and infectious diseases.

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As the time draws near for the annual J.P. Morgan Global Healthcare Conference in San Francisco, it seems as if there has been a surge in deals for local life sciences companies. Here’s our rundown:

—Biogen Idec (NASDAQ: BIIB) agreed to pay Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) $29 million, with the potential for more payments down the road as part of a new drug development partnership. Biogen and Isis agreed to collaborate to advance an experimental drug that Isis has identified for treating spinal muscular atrophy, a rare genetic disease that causes severe muscle atrophy and weakness in newborns. The deal could eventually be worth as much as $299 million for Isis.

—Denmark’s Novo Ventures led a $30 million Series B financing for San Diego-based Elevation Pharmaceuticals to fund development of an aerosol therapy Elevation has been developing for patients living with chronic obstructive pulmonary disease (COPD). Heath Lukatch, a San Francisco-based partner of Novo Ventures told me the funding should be enough to carry development of Elevation Pharmaceutical’s aerosolized bronchodilator drug to the threshold of final-stage trials.

—San Diego-based Santarus (NASDAQ: SNTS) asked the FDA to approve its new drug application for budesonide (Uceris), an oral tablet it has been developing with Italy’s Cosmo Technologies for treating mild cases of ulcerative colitis. If the FDA accepts the new drug application for review, Santarus says it has agreed to make a $4 million milestone payment to Cosmo. Ulcerative colitis is a form of inflammatory bowel disease that causes painful inflammation and ulcers inside the colon.

—Proacta, a San Diego-based cancer-drug developer has raised $500,000 toward a $3 million round of financing, according to VentureWire. The biotech was founded at least six years ago to advance a new group of anti-cancer molecules that are active in hypoxic tissue, which were identified by researchers at New Zealand’s University of Auckland and Stanford University. The company says it has raised $43 million through two private financings, and its investors include Alta Partners, Clarus Ventures, Delphi Ventures, Endeavour Capital (New Zealand), GBS Venture Partners (Australia), Genentech, No 8 Ventures (New Zealand) and Roche.

—San Diego-based Afraxis, which is developing drugs to treat Fragile X syndrome and autism, secured $300,000 toward a $2 million round of debt, rights and securities, according to a recent regulatory filing. The startup is pursuing a … Next Page »

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