Open source cancer research | Opensource.com

Open source cancer research

Posted 01 Dec 2011 by 

Lori Mehen (Red Hat)
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When it comes to treating, curing, and preventing cancer, modern medicine has largely failed. You could argue that cancer is far too complicated to unravel in the few millenia we have been documenting it. Or that the billions we spend annually on research is far too little. Established incentives and policies that perpetuate research silos certainly seem to slow success.

Download Free eBookMedical researchers have been trained in a professional culture where secrecy reigns, where they must protect their own interests. The dominant culture discourages sharing research findings and collaborating on projects. It has become more important to protect vested interests than to take advantage of the huge collaborative network that is available in academia.

This mode of thinking is a bitter pill to swallow for the quarter of our population that will die of cancer. According to the World Health Organization, one in every four deaths is attributable to cancer.

What would happen if cancer researchers were able to adopt an open and collaborative approach like the one that has--for the last two decades--revolutionized software development? What if cancer research could be open source?

Linux has been successful because a large group of people recognized a need and agreed on a process for meeting that need. The brilliance of the open source approach is in the sheer amount of brainpower participating. The open source community shows that the collective intelligence of a network is greater than any single contributor.

While the term is attributed to software development, the idea is not. In fact, some medical research does use this methodology in the same way that Linus Torvalds and others develop open source operating systems. The Human Genome Project, for example, very successfully distributed gene-mapping in efforts to speed up the sequencing of the genome. The HGP teams published their data openly, on the Internet.

More recently, a team of Harvard researchers discovered the power of distributed research. A team led by Jay Bradner at the Dana Farber Cancer Institute discovered a small-molecule inhibitor that showed promise in its ability to interrupt the aggressive growth of cancer cells. The small-molecule inhibitor, called JQ1--after Jun Qi, the chemist who made the discovery--works by suppressing a protein (bromodomain-containing 4, or Brd4) necessary for the expression of the Myc regulator gene. It is a mutated Myc gene that is believed to be at the root of many cancers. Without Brd4, Myc remains inactive. Inhibiting Myc could be part of the key to successful cancer treatments.

With the cells from an affected patient, Bradner's group successfully grew the cancer in mice and discovered that the mice with the cancer who received the compound lived, while the mice with the cancer who didn't receive the compound rapidly perished.

Instead of operating in secrecy and guarding their work, Bradner's group shared it. They simply started mailing it to friends. They sent it to Oxford crystallographers, who sent back an informative picture that helped Dr. Bradners team to understand better how the small-molecule inhibitor works so potently against Brd4.

They mailed samples to 40 labs in the US and 30 more in Europe, encouraging these labs to use it, build upon it, and share their findings in return. As a result of this open source approach, Dr Bradner's team has learned--in less than a year--that JQ1 small-molecule inhibitor prevents the growth of leukemia, making affected cells behave like normal white blood cells. Another group reported back that multiple myeloma cells respond dramatically to JQ1.  Still another found that the inhibitor prevents adipose cells from storing fat, thus preventing fatty liver disease.

Bradner has published his findings. He has released the chemical identity of the compound, told researchers how to make it, and even offered to provide free samples to anyone in the medical research community. (If you're a researcher who'd like a sample of the JQ1 molecule, you can even contact Bradner's Lab via twitter @jaybradner.)

Bradner feels his early successes are due not only to the science, but also to the strategy. Using an open source approach, sharing the information about this molecule, and crowd-sourcing the research and the testing illustrates the opportunities that an open methodology can bring to the difficult challenges of medical research and prototype drug discovery.

In his recently released TED talk video, Dr. Bradner explains that he firmly believes that making a drug prototype freely available among researchers will help accelerate the delivery of effective cancer drugs to affected patients.

With more practice—and more familiarity with each other and this kind of collaborative research—scientists can break large, complex, time-expensive projects into smaller, achievable portions. By  spreading out those small tasks among many groups, much more work can be accomplished in a vastly reduced amount of time.

Using the old research models, Bradner’s team might have learned that JQ1 affects AML cells in the first year. But it might have been next year before they got to leukemia, and years after that before they realized it also could affect fatty liver. How many years do you think the old approach adds to the development of drugs we need today?

It is time to seriously consider a different model for scientific research–one that directly engages and benefits society, encourages open access and the free exchange of scientific information. The benefit to patients would be enormous.

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8 Comments

EDGARDO GUTIERREZ

MY NAME IS DR.EDGARDO GUTIERREZ IM A CANCER SURVIVER MY SELF AND I JUST WANT TO THANK ALL OF YOU FOR A JOB WELL DONE.

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Don

I have MDS and I think these are wonderful ideas. I am not a conspiracy theorist but I do agree that there are forces at work that will do everything possible to protect their profits. In particular chemotherapy is a billion dollar industry and it will never go down without kicking and screaming and hurting people.

The "open source" concept is probably one of the most effective ways to fight back as it makes it much more difficult to conceal any dirty tactics to hold back the type of progress that is difficult to profit as much from. But I cannot help but think the FDA and/or other organization so heavily vested in this type of thing NOT succeeding they will find ways to put up roadblocks that are difficult to pass through. They can delay or indefinitely postpone approval of anything they want to, they can specify testing conditions that cannot succeed or they can interpret any kind of side-effects, even minor or imagined ones as too dangerous. They have the power to even change the law to their advantage.

They will surely use propaganda to discredit any type of "open source" movement that threatens their power. In most peoples mind the FDA is a respect "authority" that is there to protect us and they can easily paint something like this as misguided or foolish idealism not to be taken seriously - and ultimately dangerous because people are taken in by it instead of seeking "serious" treatment.

As I say, I am not a conspiracy theorist, I do not consider them evil and I believe that in many cases they DO protect us legitimately. There is no down there are many working inside the FDA who have character. However the truth of the matter is that when really big money is involved or their authority is challenged, they are a different animal.

Sorry to be so negative, but I am very positive about this concept and I hope it succeeds. To any involved, keep up the good work!

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chrispanda

Disappointingly careless reporting - to pick just one example, according to the WHO report, only in the richest countries can a quarter of all deaths be attributed to cancer. To quote another WHO report - In low-income countries ... People predominantly die of infectious diseases: lung infections, diarrhoeal diseases, HIV/AIDS, tuberculosis, and malaria. Many academics already share information readily. There is definitely room for improvement, and the open source movement may provide some helpful insights, but sloppy and sensationalist reporting weakens the argument.

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Chris Chambers

Logically it would be best to ask if there is any reason for there not to be a Cancer Cure. As this statement seems negative then why can we not find one? In depth research indicates that there have been several, that the Cancer Industry chooses to ignore. It would seem that there are areas in Physics and Biology that need updating, as a consequence of the results of the Erganon Microscope by Dr Olbrich. An alkaline blood ph seems to be at the root of documented cures by Dr Simoncini and Rife, and there are others based on phytochemicals. Indeed nothing less than a wholesale revolution in Medicine and Science seems to almost be upon us.
BSc Physics, ARCS

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DrZZ

The are plenty of examples of freely available data related to cancer and other diseases. At NCI data for hundreds of thousands of structures (including most of the approved agents), in vitro and in vivo antitumor data are available (see http://dtp.cancer.gov/webdata.html and http://dtp.cancer.gov/docs/dtp_search.html). There is also gene expression data (http://dtp.cancer.gov/mtargets/mt_index.html and http://cgap.nci.nih.gov/). More broadly there is PubChem (http://www.ncbi.nlm.nih.gov/pcassay) with millions of compounds and thousands of bioassays. It is being fed in part by the Molecular Libraries Program (https://commonfund.nih.gov/molecularlibraries/) where agreeing to promptly put the high throughput screening data in PubChem is a requirement for the assay to be accepted in the program. There is far more openly data available than is being used.

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RPR

Nice article. Beside the specific research context (cancer research), I like the basic message that I can see in it: in research collaboration pays more than competition (in terms of knowledge accumulated and benefit for the society).
Unfortunately, today the opposite philosophy that forces researchers to compete each other is gaining consensus.
A personal example: here in Italy there is a proposal by the ANVUR (National Association for the Evaluation of Research and University, more or less) according to which only the top 25% of professors (according to some evaluation method still to be defined) will be able to have PhD students. This makes all my colleagues competitors of mine. (Note that having PhD students is not a prize, but a necessity of research work.) Until now, if a colleague of mine asked me for, say, a piece of software that my group developed, I would have given it to him without any problem. He would have done some research, published some papers that referred to my work. Everything would have been fine. Now, with this competitive approach, I am not sure if it would be good for me give the software to my colleague since he would get an advantage exploiting my work, and every paper that he will publish will be a little backward step for me. In the end we risk of getting a research community made of little "monads" that do not talk each other.
Who proposes the competitive approach says that it is necessary to introduce some feedback in the system in order to avoid the presence of free-loaders. Although I agree that there is a risk of getting free-loaders aboard if no control is done, I believe that the ultra-competitive approach is too strong a solution. Note that "getting rid of free-loaders" is not the same of "allowing to just 25% of researchers to do their work."

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Unidentified

Unfortunately I think there is a fundamental assumption in this article that people choose research for the right reasons. After twenty years in academia, I can tell you that publishing and winning research funding is the name of the game - what a disaster it would be to solve this crisis. Where would the state of tenure be without cancer, HIV and other serious illnesses? I'm sorry for the pessimism, but I think your rose colored glasses are making you assume that the group of researcher who publish or perish and have infinity pools put in their gardens thanks to their tenured positions and salaries actually want to change the world.

Want to see real-life 50 MILLION dollar collaboration at work in a Research 1? Try iPLANT...50 MILLION folks from NSF and done NOTHING, ueber-NOTHING for the past five years, with a possibility of a five year renewal. After ten years time, they will still have done nothing. The only people benefiting from this project are the ones getting HUGE salaries from the NSF - now that's what I call (taxpayer) collaboration. You should check it out. Let's see MD researchers at that same institution are making 425K, and their ability to maintain those positions requires the development of largely patented technologies.

The system, as it is, will NOT support this type of idea. Sorry. First change the system that promotes greed and profiteering through academic and especially scientific and medical research. My two cents.

"Disgruntled" in the US.

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markchu2011
Community Member

Thank you for this information. It adds my knowledge about cancer. God bless!

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