Scientists Report Advance in Drug Repurposing

For most of recorded history, medicine has been qualitative in nature, relying on subjective feedback from patients and anecdotal prescriptions from physicians. Medicine today is becoming more and more quantitative in nature. The Wall Street Journal yesterday reported what they described as “high-tech recycling”, where researchers have developed an innovative way to use already-approved drugs that have been used to treat a particular disease to work on diseases they were not intended to combat (see Scientists Report Advance in Drug Repurposing – WSJ.com).

Using a computer science technology called high-throughput computing (HTC), researchers were able to scan National Institutes of Health public databases containing the results of thousands of genomic studies to focus on 100 diseases and 164 drugs where normal and diseased tissue samples, drugged and not drugged, were compared. The program then looked for cases where a drug created a change in gene activity that was opposite to the gene activity caused by a disease, on the hunch that this might indicate the drug could be an effective treatment. For example, suppose a patient had a problem with their liver and the cause was an abnormality of the ABC gene. The XYZ drug used to treat heart problems happens to have an effect that corrects the abnormality of the ABC gene. Even though the XYZ drug was designed for heart problems, it may also be a cure for a liver problem. A real example is that researchers found that cimetidine, an ulcer drug, might be effective in treating lung cancer. I believe that the bioinformatic merger of biology and computer science is likely to change the practice of medicine more in the next decade than all of the changes of the past century.

Tags: bioinformatics, genetics, high-throughput computing, htc, medicine

Strawberries

There are a lot of subjects I do not know much about. One of them is genomics. I moderated a panel at a technology conference a few years ago that included three PhDs in bioinformatics and I learned enough to confirm how little I knew. I asked the three experts what book would enlighten me. They unanimously recommended Genome: The Autobiography of a Species in 23 Chapters by Matt Ridley. After reading the book I was convinced that the amount I did not know was orders of magnitude greater than I had thought. One thing I do know is that genomics is going to have a very major impact on healthcare in the years ahead — more like months than decades.

An early indicator of what lies ahead might be what is going on with fruits and vegetables. Elizabeth Weise, Science writer at USA Today, just did a nice summary of the latest genomic breakthrough with strawberries. Her story, Woodland strawberry genome sequenced, is about the genome of the woodland strawberry, a “cousin” to today’s cultivated strawberry, that has now been sequenced by an international research consortium.

The strawberry is the second smallest plant genome to be sequenced, with just 14 chromosomes. What sequencing means in layman terms is that the researchers have been able to construct a “parts list” of the strawberry. (See the actual gene mapping in Nature Genetics if you are curious about the details). Weise reports that as a result of the sequencing, breeders may be able to create tastier and hardier varieties of the popular berry as well as for other crops in its family, including almonds, apples, peaches, cherries and raspberries. The researchers are optimistic that they will also find new “parts” that will provide resistance to strawberry wilt, a common, soil-borne pathogen that spoils cultivated strawberries.

The consequences for humans are mind boggling. Gene hunters are finding more genes and linking them to diseases and predispositions to diseases. The next phase will be developing methods of prevention and cures. We may see more breakthroughs in the next ten years than we have seen in the last 100 years. If you want to get an idea of the scope of the human genome project, I recommend reading Medical and Societal Consequences of the Human Genome Project by Francis S. Collins.

Tags: bioinformatics, francis collins, gene mapping, genome, Genomics, health care, Healthcare, john patrick, matt ridley, strawberry

Back to School

The grandkids have their backpacks loaded up. I hate to see them bent over hauling many pounds of books and look forward to the day when they have just a Kindle and some wholesome snacks in their backpacks with room to spare. The four grown children are thankfully gainfully employed but two of them are back in school to advance themselves. Believe it or not, Pop Pop is also in the mix.

I have been thinking about a doctorate for years. I have been fortunate to be able to earn a good education during my life, including three degrees, but I have a personal desire to achieve the pinnacle of education and use it to make an impact on something I am passionate about — healthcare. My education and career up until now have been heavily focused on technology. I believe that in the near future there will be a merger in the healthcare field of traditional information technology and clinical information technology. Bioinformatics will make personalized medicine a reality and we will no longer have to rely on anecdotal medicine. It will not be long until the healthcare information technology industry will be larger than the IT industry as we know it today. I want to be part of this revolution. By combining my information technology experience with a new focus on healthcare I believe that as a doctor of health administration I can help develop techniques that can improve healthcare outcomes and quality of life for many people.

Having been a member of the board of the regional hospital near where I live and having participated as a member of the planning, technology and medical affairs committees, I have been able to learn a lot and have become passionate about the key issues and opportunities that lie ahead. I plan to focus my dissertation on the intersection of the Internet, mobile computing, video chat, and remote primary care for patients. More on this as things develop.

Studying for a degree using the Internet as the classroom is hardly a new idea. When IBM made forays int0 this area years ago it was called “distance learning”. Some call it e-learning. I call it the natural way to learn. Whatever you call it, e-learning has come a long way. Over the last ten years I have looked at various programs that are offered. Most universities have some form of e-learning but the one I found to have the broadest and deepest commitment is University of Phoenix. For them it is big business — $4 billion in revenue and $600 million in profit last year. I was particularly impressed with their doctoral program. They follow what their School for Advance Studies calls the scholar, practitioner, leader model. The idea is to combine scholarship and theory with practical skills and knowledge that you can use in the workplace. The course work is almost entirely online but there are three intense week-long residencies during the next three years to support and expand on the education received online.

Being a student again fits well with e-tirement. I started on August 31 and have been doing research, writing papers, and participating in the online forums. So far, so good. The journey has begun. No turning back. Wish me luck! Oh, and if you don’t see an many posts here, rest assured I am posting scholarly work in the online classroom.

Index of stores about My Doctoral Journey

Tags: bioinformatics, dha, doctor of health administration, e-learning, facetime, health information technology, hospital, video