Hacking For A Cure: Innovative Scientists Fill Federal Research Gaps

Hacking For A Cure: Innovative Scientists Fill Federal Research Gaps
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Lyme disease is caused by a syphilis-like bacterium that is transmitted primarily via tick bites. If treated immediately, many people experience nothing much more than a bad flu. Undiagnosed and untreated Lyme disease, like untreated syphilis, often becomes an infection of the brain and nervous system that can cause numbness, nerve pain, neuropsychiatric disorders including depression, panic attacks and dementia-like cognitive impairment, and in severe cases it can cause paralysis.

That's where the consensus ends. Many scientists and entities that establish and enforce medical treatment guidelines, including the Infectious Diseases Society of America and the U.S. Centers for Disease Control, claim that -- as with syphilis -- treatment with antibiotics permanently kills off all Lyme disease bacteria and should resolve all Lyme symptoms.

Patients who have been diagnosed with and treated for late-stage Lyme, however, frequently claim that the symptoms not only persist but become progressively worse; indeed, it is not rare for Lyme to be mistaken for ALS, multiple sclerosis, lupus, rheumatoid arthritis or other autoimmune diseases.

These patients are desperate for a cure, and with over 300,000 Americans contracting Lyme disease each year, the demand for greater understanding of the disease is rising sharply. Each year, the National Institutes of Health dedicates approximately $24 million for Lyme disease research; by comparison, Zika virus (which has just been found to infect the brain and can evade the immune system, not unlike Lyme) likely will receive up to $1 billion in researching funding from NIH this year. As of today, Zika has affected 756 Americans, none of whom contracted it on American soil. While the severity of Zika demands research, so does the severity of Lyme -- yet the federal government, for reasons so far unexplained, has not determined Lyme to be anymore a priority than headaches, for which it also invests $24 million per year in research funding.

Enter the Lyme Innovation hackathon. This past weekend, Harvard Medical School's Dean Center for Tickborne Illness, in partnership with the VA Center for Innovation, MIT Hacking Medicine, the Open Medicine Institute, and sponsored by the Bay Area Lyme Foundation, will convene a three-day "hackathon." This event calls on the public "to solve critical prevention, diagnostic, and treatment and rehabilitation challenges facing the Lyme disease field by bringing together diverse researchers and scientists."

Before the event, I spoke with Andreas M. Kogelnik, M.D., Ph.D., director of the Open Medical Institute, about why this hackathon is necessary and what he hopes for it to accomplish.

What is the hackathon, and what do you want to accomplish with it?

I'm actually an infectious disease doctor, but I'm also a computer science data nerd. I was at Stanford for about eight years chomping away at 'How do we define illnesses on a molecular level?' because it turns out we don't do that very well in clinical medicine. Also, how do we use molecular testing of all sorts to start to do that?

As I was seeing patients and doing research on those patients, I ran headlong into chronic fatigue syndrome, which was my first long-term exposure with any chronic illness. It opened my eyes up to this whole, for lack of a better word, diaspora of chronic neuro-immune illnesses -- I put Lyme in that bucket.

There's this whole host of conditions that are either triggered by an infection, as they are themselves an infection, like Lyme or Bartonella. Or we just don't even know yet... people think there's an autoimmune component. But all of them circle around the immune system and metabolism and some of them around pathogens [that cause] major dysfunction at multiple levels of the body, becoming chronic in many cases.

So I was fascinated by this, and I said... if there's any patient group that needs analysis and redefinition more, this is one of them. I started meeting a lot of people in the field and getting into the controversies with different conditions, be it Lyme, chronic fatigue or other related conditions. I realized there was this huge gap between what is happening to patients and what should be happening in the medical field.

It was a story that, to me, represented some of the critical breakdowns in our healthcare system in terms of not just patient suffering, but economically and outcome-wise, that we are not dealing with these illnesses properly. It costs patients a lot and it costs society a lot. So we started asking how we can drive toward a better answer, and the obvious answer to me was to use more and better data. So we started the Open Medicine Institute out of Stanford with that in mind, and one of the goals was to create systems by which we can easily collect data directly from patients or through any other source, tying back to new biotechnologies that we can use to measure the immune system or different pathogens, or measure metabolically what's going on in the body. In doing so, we started connecting different Lyme doctors, academic centers and so forth. We are looking at doing studies with them, working with people at Stanford, Mass General and the community sites. We all came to an accord around the need to collect data.

I give talks around the country, and one of my tag lines is, "As physicians, we're data stupid." We don't have enough data around our patients in many patients, particularly around complex illnesses. I would put Lyme front and center as one of those cases. People stand on a lot of pedestals talking about stuff when they really don't have much data about it, on all sides of the fence. A lot of positions are determined by where people stand on their thought processes. We need more, better data on these things... and put aside all this political nonsense.

Patients are sick and there's no question that a lot of them are really, really sick and that needs to be addressed.

So the hackathon is a response to that. The OMI embraces it, and there's White House support for it, Mass General and other places. So part of what we're trying to do with the hackathon, with OMI, and with multiple medical disciplines in general, is to start to raise some awareness and better data, to get people to start thinking outside the box in medicine and particularly around Lyme disease.

It turns out that there's a tremendous number of stones that have not been looked under. It hasn't happened in a lot of conditions, and I think that patient activism and engagement with research in particular is really coming into its own and driving transparency in medicine -- but we've got a long way to go. So the hackathon is one small step in getting on that road and hopefully getting a lot of patients a lot better information.

Who exactly is doing the hacking?

Anyone who has an expertise that can be applied. Anyone who has the gumption and desire to try to make a difference. A lot of groups that engage on this are not necessarily clinically vetted in terms of having a clinical background. It's basically engineering types a lot of the time, but we'll get a cross section of folks. Some people will have a particular expertise, whether it's data science or something from their day jobs. When we did one in Boston, there was an art therapist who had an idea around how applying that around the mental health side of the disease who had an idea about how to use data to provide better patient support. So there's all kinds of opportunity for anyone to participate, not just someone with a computer science degree.

Last month, there was a Lyme science and policy forum on Capitol Hill. While the room was full, the event didn't attract a single congressional staffer. The forum ended up being a lot of preaching to the choir -- a choir of patients with severe, progressive Lyme disease who traveled to Washington to ask for greater investment in research. So they would find it encouraging that the White House and Department of Veterans Affairs are invested in the hackathon.

In what way is the White House supporting the hackathon? Is it a vote-of-confidence type of support or is the support financial?

It's more than just a vote of confidence. They're actually helping to sponsor some of these events. I think there was a small grant that was given to the Harvard team to set up -- I don't know if it was from the White House or from Bay Area Lyme Foundation -- but the White House is very engaged in the National Day of Civic Hacking. I imagine there was some involvement there at that level, you know, they want to engage the citizens around anything and everything that's important to them and so somebody suggested Lyme disease and it stuck.

What's the involvement of the Department of Veterans Affairs?

They're interested in that it affects many of their patients. The VA department that was affected a lot was the mental health department because there's a lot of mental health issues -- depression and so forth -- that go along with chronic disease. I can't speak for them directly, but my sense is that they are interested in a broad level, that they have little crises going on because of the downstream effect of Lyme disease. They're interested in helping to solve that, and I think that's terrific.

Regarding the controversy surrounding chronic or persisting Lyme disease, there is a bitterly divided argument, with the Infectious Diseases Society of America (IDSA) and the U.S. Centers for Disease Control and Prevention (CDC) on one side and Lyme disease patients, physicians who specialize in Lyme disease, and the International Lyme and Associated Diseases Society (ILADS) on the other. The IDSA and CDC claim that all Lyme infections are cured with two to four weeks of doxycycline, but Lyme patients and their doctors insist that Lyme symptoms sometimes persist and worsen following the discontinuation of antibiotic treatment.

The CDC refers to recurring symptoms as "post-treatment Lyme disease syndrome," and suggests patients who experience ongoing symptoms get screened for other illnesses and that they "maintain a healthy diet and get plenty of rest" and "share your feelings... it doesn't mean that your symptoms are not real. It means that you are a human being who needs extra support in a time of need. The IDSA says that "the term chronic lyme disease is applied very liberally... for symptoms that aren't explained" and that "chronic Lyme disease is not based on scientific fact." In a video on the IDSA website, Dr. Paul Auwaerter says that "many patients... didn't have any laboratory test, any history of rash that seems to confirm this diagnosis," yet many patients who tested positive for Lyme disease and who had the characteristic rash and were subsequently treated with short-term antibiotics report that they improved temporarily, and then experienced degenerating health following discontinuation of treatment. Many of these patients feel that advice to "share your feelings" is dismissive and inadequate for the severe, progressive chronic health condition they live with.

As an infectious disease specialist, where do you stand on this? Is it irrational to consider, for example, that the human body is a highly complex collection of neurons that are more sensitive and more advanced than man-made medical laboratory equipment, and that the growing number of patients who report worsening physical health may be experiencing a progressive disease? Or are existing laboratory tests that are available today more reliable indicators of wellness than are human bodies?

Google "quantified self." There's a big focus on this here in the Bay Area, where people are measuring themselves for all kinds of things. A lot of them are fitness nuts who want to know how far they ran, how many calories they've burned and so forth. And there's a lot of this happening now around disease. We support that.

What you describe happens all the time, unfortunately. It's the hubris of medicine, right? I'm a doctor, so I'm allowed to say this: We think we know it all. We have to learn a new vocabulary in medicine because you patients don't understand what the hell we're talking about. There's a word in that vocabulary that means "we don't know"--just because we're afraid to say we don't know.

The average patient visit with a physician has gone from 30-plus minutes a decade ago to about four minutes today. In four minutes, you can't even barely say hello to somebody let alone deal with a chronic illness -- neuro-immune, Lyme, whatever you want to call it. So the system itself has bred an inability to care for these diseases, and so rather than saying "I don't know" or "we can't help you at this time," we shuffle them off to specialists to deal with the problem that way, and so the core problem doesn't get addressed. That is part of the message here: there's no incentive for a physician to handle this properly. The system itself is telling them, "get the patient in, get the patient out, and deal with their acute problem." The incentives are set up that way. We don't deal with chronic disease very well in the healthcare systems today -- and we're not trained to deal with it. Some egos build up around given diseases, and when you start to talk about a new aspect of an existing condition, that can be hard for some people to take. And they protect their turf because they want to be experts on that turf. The patient of all people is trying to take their turf--God forbid. So it's a conundrum that we have to get past. We have to start thinking in medicine about chronic disease rather than short-term Band-Aid fixing. The only way to get past that is to have good data and good science and investigation, which includes the patient voice in there. There's a lot that happens in the three months between doctors' visits, and we need to get that data. We need to make everything as quantifiable as possible, and not forget that we don't know everything about medicine.

At the end of the day, it is what the patient tells us that defines what patients are experiencing, very specifically, actually. We need to listen to that.

Like many other people, I went through the mill of doctors -- all of them very concerned at first. They ran labs, neurologists found several "worrisome" abnormalities, but nothing that added up to anything conclusive. And so, I was dismissed, more than once at the suggestion that my symptoms either were due to an overactive imagination or anxiety. And this conclusion is reported commonly -- perhaps more frequently than not -- among Lyme disease patients. So many of us discover something that we didn't know about medicine today: most doctors are not interested in investigating illness, only in diagnosing what is already known, and dismissing anything that is not already well understood.

So of the hackathons that you've had so far, have there been any projects or investigations that are promising insofar as improving the understanding of Lyme disease, or its diagnosis or treatment?

The initial hackathon was not really intended that way; it was intended as a way to get ideas. The second round that's going to happen in a couple of weeks... there's actually prize money at stake, and the top five or 10 teams will get several thousand dollars each, and in the fall a winning team will get a bigger award, and that one will move to a practical realization. We have a very practical bent on this, that things really need to move in terms of practical outcomes. In some ways, the hackathon is about getting things rolling, and that one of the organizations involved will get on board and move to a clinical trial. But for now, it's too early for that.

You've discussed the role of philanthropies in these efforts. It seems like there's a major funding disparity with respect to the federal resources allocated for Lyme disease research. The CDC estimates nearly 330,000 new cases of Lyme per year, and NIH dedicates $24 million to researching Lyme each year. By contrast, there are about 2,000 cases of West Nile virus each year, and the NIH dedicates $42 million to it. And now Zika virus has become the government's priority, with 618 Americans affected to date and $622 million to $1.9 billion of federal research dollars being proposed. That's $72 per Lyme patient, $21,000 per West Nile patient, and $1 million to $3 million per Zika patient. Obviously, every infectious disease should be researched, but as the third most prevalent infectious disease in the country, why is Lyme so disproportionately underfunded? Will this change, or will philanthropies and private entities have to bear the full burden of research?

I think there's some movement there, but those ships turn slowly. The CDC upgrading its estimate [in 2013 from 30,000 new cases of Lyme per year to approximately 300,000 new cases per year] by an order of magnitude that's unheard of -- I don't know of any other disease where they've corrected their estimate by such an order of magnitude. It's crazy. It's just crazy. So that was a big deal, make no mistake. Pushing that into the mainstream is in part a major step that needs to happen. The most important pieces of that are in some sense activism. At the end of the day, we are the ones who set the agenda for our congressfolk and it's a tough area for patients to become activists because they're so sick.

Politicians are hearing different stories and don't know what to believe, so the scientists who are already established are getting heard. But that tide is changing. The advocacy aspect has improved a lot in the last couple of years, but it has a long way to go for sure. To drive that conversation, we have to have good data, but the system is broken in terms of collecting that data. It's a real catch-22. But the collaborative efforts are starting to break that open because there is a huge economic burden on our society.

And that economic burden seems impossible to quantify at the moment because there are so many undiagnosed cases, misdiagnosed cases, unreported cases...

If you look at the politics of medicine, the same kind of thing happened with Heliobacter pylori infection. Marshall thirty years ago was laughed out of the room for a good chunk of his career until he proved that H. pylori causes ulcers -- and then he got a Nobel Prize for it. And, you know, everybody stopped laughing. That becomes part of the narrative, a critical piece of understanding -- you have to have a mechanism for innovative thoughts to stand up like Marshall did for H. pylori. It's time to have innovation around Lyme disease.

The Lyme Disease hackathon took place June 17-19 at the Microsoft Nerd Center in Cambridge, Massachusetts.