If Allegro Diagnostics’ clinical trials go as planned, the Maynard, Mass.-based company will be on its way to commercializing a test to detect the "canary in the coal mine" of the planet’s deadliest cancer: Early-stage lung cancer.

With a patented molecular diagnostic assay, Allegro co-founder and Boston University associate professor Avrum Spira has garnered over $3.5 million in funding from the National Institutes of Health and $8.9 million from investors.

Shortly after being named BU’s Innovator of the Year for 2011, Spira took time to speak with MassDevice about the foundation of the company, its progress toward getting the test to market and the future of cancer diagnostics.

MassDevice: What was the inspiration for Allegro Diagnostics?

Avrum Spira: For the last 10 years, my lab over at the [Boston University] medical school has been focused on developing ways to diagnose lung cancer at an earlier stage.

Lung cancer is a deadly disease; it’s the number one cause of cancer death in the United States and in the world, and as a pulmonary doctor I always see tremendous numbers of cases of patients who are dying.

One of the main reasons they die of the disease is we don’t detect it at an early stage. We pick it up when it’s already advanced and the patients aren’t going to survive very much longer. So clearly there was a clinical need to develop the tools to identify smokers who are mostly likely to develop the disease and pick it up at an early and potentially curable stage.

That was really the motivation for all the molecular biomarker work that our group has been pursuing for the past 10 years.

About five years ago, we had a major breakthrough in our research, where we identified a molecular signature in airway cells, in the cells that line your windpipe. What was interesting is that signature could distinguish a smoker who was going on to get lung cancer from one who was not.

One of the reasons it’s hard to diagnose lung cancer early is the cancer arises deep in your lungs, so it’s very hard to get to that without opening up your chest in surgery. These cells that line your windpipe are almost like a canary in a coal mine.

By looking at the genetic molecular changes in those cells, cells that look normal under a microscope, and yet the molecular changes in those cells provide us with a signature that you’re either on the way to getting cancer or not, to give us an opportunity to identify the disease at an early and potentially curable stage.

That was a major breakthrough for us. We published that in a very high-impact journal and the patents that went along with that are essentially what gave rise to Allegro Diagnostics. The idea at that point, in 2007, was we now believe that we have a biomarker that can impact clinical practice, can help diagnose the disease early – how do we get it into the clinic?

That’s when Boston University came up to us and said, "Hey, you’ve got some patents that are commercializable, we can give you the help to take this biomarker from an academic project to move it into the clinic," and that’s essentially what Allegro Diagnostics is trying to do.

MassDevice: What is Allegro working on now?

AS: We’re in the middle of a large clinical trial to validate this 80-gene biomarker. What we have is an assay that measures the activity level of a set of genes in the cells in the windpipe. That’s now being validated on about 800 smokers who are getting bronchoscopy, which is a procedure that’s been used to diagnose lung cancer in people who have abnormalities on their imaging studies of their chest.

So what they’re to do is see if our biomarker accurately distinguishes those people who truly have lung cancer from those who don’t. If it does, it can serve as an adjunct procedure to bronchoscopy, so people getting that procedure can also have this molecular study done to improve the accuracy of diagnosing lung cancer in that setting.

I should mention bronchoscopy doesn’t do a very good job on its own in detecting lung cancer. That’s why we need to have additional molecular tools added on.

MassDevice: So this doesn’t replace bronchoscopy, it adds on to it?

AS: It actually relies on the procedure to get the cells in the windpipe. So these are patients who are going to get that procedure anyway, as an initial diagnostic test. That test has a very relatively low sensitivity for early-stage lung cancer, because it can’t get all the way out deep into the lung and it has a very hard time in finding cancer cells.

Our test is essentially piggy-backing on that study. We’ll just brush the cells in the windpipe on the way out, at the end of the procedure, look at the molecular changes there, and we’ll tell you whether that abnormality on that CT scan is cancer or not.

That can help the clinician then decide, do I go to surgery next or can I just watch the patient with a routine CT scanner? That’s the specific clinical indication that we’re looking for.

MassDevice: What’s the next step?

AS: The next step is to complete the trial. It’s about halfway through. We’re hoping, within the next 12 months, to finish the quota of patients, run the biomarker assay, validate the accuracy and then hopefully offer the test, maybe initially as a CLIA, but eventually go through the FDA and get this as a true FDA -approved biomarker into the clinic.

We do have additional biomarkers in the R&D phase back in our lab. Specifically, we’re trying to move biomarkers to a less-invasive site.

We believe that the cells that line the nose and potentially the mouth could also serve as this "canary in the coal mine," that molecular changes there might tell whether a smoker’s developing lung cancer.

We’re beginning to explore that in a very early discovery phase. Hopefully that’s something Allegro will take on as its next product.

MassDevice: What do you see for the future in molecular diagnostics?

AS: I think, in the next five to 10 years, we’re going to see a number of these types of tools make it into the clinic and impact care. It’s exciting as a clinician, because these are diseases that we have done very little for in 20, 30 years, and we’re at a sort of breaking point now of a new molecular revolution in how we manage these diseases clinically. It’s very exciting.