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Foundation Medicine Raises $25M to Get to the Bottom of Cancer Genomes

Xconomy Boston — 

The trick to beating cancer could be a single test that shows all known genetic traits in each person’s tumor, and that also matches those results to the best treatments. Boston-based Foundation Medicine reports today that it has raised the first part of a planned $25 million round of Series A venture funding to make comprehensive genomic analyses of tumors a standard tool in the fight against cancer.

A crack team of cancer, genetics, and industry veterans from the Boston area has assembled around the startup. Boston-based Third Rock Ventures, founded by former executives of the cancer drugmaker Millennium Pharmaceuticals, has incubated the company and led the first-round financing. Alexis Borisy, an entrepreneur-in-residence at Third Rock and the former CEO of Cambridge-based CombinatoRx (NASDAQ:CRXX), is the startup’s founding chief executive (something we were the first to report back in February). And Eric Lander, a pioneer of genomics research and an advisor to President Barack Obama on science and technology policy, is headlining the group of scientists and physicians who are advising the startup.

Foundation Medicine, which was formed in 2009, has come into being as high-speed DNA sequencing and a slew of academic studies help to uncover new genetic mutations that, say, protect tumors from certain therapies, or help cancer cells grow out of control. Drug companies are developing cancer drugs for patients who have specific genes that make them likely to respond well to the treatments, building on Roche-Genentech’s success in marketing the breast cancer drug trastuzumab (Herceptin) for women with the HER2 gene. Also, a growing number of startups are focusing on providing new genetic tests that help guide physicians in treating cancer patients.

Foundation Medicine is taking its own approach to personalizing cancer treatments. While many previous firms have focused on developing tests to detect specific genes linked to likely outcomes of cancer treatments, Foundation Medicine is planning to use high-throughput DNA sequencing technologies to expose the plethora of genes and genetic variants in cancer genomes, according to Borisy. Borisy and Third Rock are betting that the future of cancer treatment will involve a single analysis of cancer DNA in guiding treatments, rather than multiple tests that screen for individual genes or groups of genes.

Today DNA sequencing is done primarily in research settings, with extremely limited clinical use. Borisy, however, says that it’s time to put this technology to work for people with cancer. “If many patients would benefit from this deep understanding, then there needs to be a way to take this from being a research tool to something that would be useful and meaningful and work in the routine practice of clinical oncology,” he says. “That has been the driving motivation and inspiration behind Foundation, and it’s quite clear that this is the way the world is going.”

The company’s exact strategy is evolving, according to Borisy, yet some details are clear. The firm plans to set up a central lab in the Boston area where the DNA from patients’ tumor samples will be sequenced. With the resulting data, the firm will use its internal expertise in genomics and cancer biology to highlight which genetic variants are present in the tumor and their implications on treatment options. (Borisy declined to say how much the service would cost, but he did indicate that it would not cost tens of thousands of dollars.) The company plans to provide reports on its findings to oncologists and its other customers, who can access the information on a secure website that protects the information from unauthorized viewers. The physician could then use the information to make treatment decisions, or a pharmaceutical company could use the data to decide which patients to include in a clinical trial.

In the past, it would have been difficult to make treatment decisions based on sequenced cancer DNA due to a lack of knowing the roles of many genes. But that’s rapidly changing. The National Institutes of Health announced in September that it’s spending $275 million from agency budgets and federal stimulus funding to map 20 different cancer genomes over the next two years, in a program called The Cancer Genome Atlas. (In fact, one of Foundation Medicine’s founding academic advisors, Matthew Meyerson, is one of the lead researchers involved in The Cancer Genome Atlas.)

There’s already been growing use of genetic tests to guide cancer therapy. Redwood City, CA-based Genomic Health (NASDAQ:GHDX), for example, reported that its annual revenue rose from $110.6 million in 2008 to $149.5 million last year, based on a 35-percent jump in sales of its genetic test to predict which patients with breast cancer would likely benefit from chemotherapy. A number of startups in the Boston area such as Immuneering, Predictive Biosciences, and On-Q-ity are also developing ways to match patients with appropriate cancer drugs.

“I think people are on board with the concept of personalized medicine,” says Ben Zeskind, the founder and CEO of Cambridge-based Immuneering, which uses computer models to simulate interactions between drugs and patients’ immune cells to predict whether they would benefit from certain drugs for cancer or other diseases. “The future of fighting disease is going to be about targeting therapies very specifically to the patient and to a likely response [to therapies].”

There also are plenty of high-profile people who agree with the way Foundation Medicine is approaching this opportunity. The company’s board of directors includes Third Rock partners Mark Levin and Robert Tepper, the former CEO and chief scientist at Millennium (now called Millennium: the Takeda Oncology Company), Borisy, and David Schenkein, the chief executive of the Cambridge-based cancer drug developer Agios Pharmaceuticals, who was previously a leader of cancer drug research at the biotech powerhouse Genentech. The scientific advisors are Lander, a founding director at the Broad Institute of MIT and Harvard; Todd Golub, a Broad Institute founder who also researches cancer genetics at the Dana-Farber Cancer Institute; Matthew Meyerson, director of Dana-Farber’s Center for Cancer Genome Discovery; and Levi Garraway, a member of Dana-Farber’s Center for Cancer Genome Discovery.

This is a lot of brainpower and experience behind Foundation Medicine. And the firm now has money in the bank to grow its operations, which are expected to include 30 to 40 employees by the end of the year, according to Borisy. Still, the company is going to have to prove the utility of its approach to get health insurers to provide reimbursements for its service, and to make sequencing the genomes of individual patients’ tumors a routine part of treating cancer.

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  • gpawelski

    Most cancer patients won’t benefit from molecular profiling.

    Molecular profiling examines a single process within the cell or relatively small number of processes. All the gene mutation or amplification studies can tell is whether or not the cells are potentially susceptible to a mechanism of attack. The aim is to tell if there is a theoretical predisposition to drug response. It doesn’t tell you the effectiveness of one drug (or combination) or any other drug which may target this in the individual. There are differences.

    There are many mechanisms/pathways to altered cellular function. I believe functional tumor cell profiling would be more beneficial. It measures what happens at the end, rather than the status of the individual mechanisms/pathways. It assesses the activity of a drug (or combinations) upon combined effect of all cellular processes, using combined metabolic and morphologic endpoints, at the cell population level, measuring the interaction of the entire genome.

    Cancer is a complex disease and needs to be attacked on many fronts.

    What is needed is to measure the net effect of all processes within the cancer, acting with and against each other in real time, and test living (fresh) cells actually exposed to drugs and drug combinations of interest. The key to understanding the genome is understanding how cells work. How is the cell being killed regardless of the mechanism.

    Cancer cells often have many mutations in many different pathways, so even if one route is shut down by a targeted treatment, the cancer cell may be able to use other routes. Targeting one pathway may not be as effective as targeting multiple pathways in a cancer cell.

    Functional tumor cell profiling tests additional drug concentrations for the “targeted” agents, some of which have very steep dose response relationships (unexpected toxicities such as the recently described microangiopathic hemolytic anemia that can occur from the Sutent/Avastin combination). Should patients knowingly take the unknown risks of combination therapy that is known to work well in vitro against their tumor?

    Another challenge is to identify for which patients the targeted treatment will be effective. Tumors can become resistant to a targeted treatment, or the drug no longer works, even if it has previously been effective in shrinking a tumor. Drugs are combined with existing ones to target the tumor more effectively. Most cancers cannot be effectively treated with targeted drugs alone.