Science News: Disease Reference Guides

While the media seems to announce medical breakthroughs all the time, for the patient, the pace of progress can seem excruciatingly slow. It takes time for science to turn into treatment. But some months are better than others, and in Sept. 2012, more than 30 papers were published in scientific journals, including Nature and Science, that explain how scientists’ collaborative efforts are making headway into uncharted parts of the human body toward a common goal of mapping and curing disease.

An Atlas of Breast Cancer

In the United States alone, 35,000 women fall victim to breast cancer each year. Globally, there are 1.3 million new cases and 450,000 deaths annually. The National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) collaborated to create the Cancer Genome Atlas (TCGA), a comprehensive catalog of the changes, or errors, that occur in DNA and cause and direct the hundreds of different kinds of cancer. Scientists, mining the data wealth that is centralized in this atlas, have recently made important discoveries that will impact the prevention, detection, and treatment of breast cancer, as well as other kinds of cancer.

Each cancer has its own DNA, or genome. In the analyzing of the genomic data gleaned from breast cancer tissue, scientists have confirmed four primary and unique subtypes: HER2-enriched (HER2E), Luminal A (LumA), Luminal B (LumB) and Basal-like. Each one of these kinds of cancers has its own “road map”-a unique composition with its own path of treatment and outcome. What so surprised the scientists was the discovery that the basal-like breast tumors, found in what is often called Triple Negative Breast Cancer, shares more in common molecularly with serous ovarian tumors than with the other breast cancers.

What this tells us is that greater understanding and best practices are to be sought within the greater atlas, not just the chapter on “breast” cancer. It is less about where the cancer is found, but more about where the cancer came from.  There is a scientific shift away from where the cancer is born, to how it was born and under what circumstances it will thrive.

An Encyclopedia of DNA

Ten years ago, the Human Genome Project successfully mapped human DNA. The assumption has been that the proteins of our DNA are the important, or “good” stuff, while the rest, the dark matter, is basically junk. Not so. Thanks to the Encyclopedia of DNA Elements study (ENCODE), scientists have discovered that that so-called junk is packed full of gene switches that, taken cumulatively, tell the cells of the body what to do.

For instance, in the case of autoimmune diseases such as lupus, rheumatoid arthritis, and Crohn’s disease, the switches seem to lie in the immune cells; while the switches for diabetes, cholesterol, and metabolic issues are found in liver cells. Instead of looking to the genes themselves for disease causation, this discovery redirects us to the parts of our DNA that control how our genes behave.  In the New York Times, Eric Lander, president and founding director of the Broad Institute of Harvard and the Massachusetts Institute of Technology, likens the potential of this discovery to Google maps;  the Human Genome Project  ‘‘was like getting a picture of earth from space,” but ‘‘It doesn’t tell you where the roads are, it doesn’t tell you what traffic is like at what time of the day, it doesn’t tell you where the good restaurants are, or the hospitals or the cities or the rivers.’’

With at least 4 million switches per genome, the task of “mapping” the switches in an encyclopedic way is monumental. Brad Bernstein, an Encode collaborator explains: “We now have a map of the genomic locations of these switches, but we don't have a map showing which switch controls which gene.” And, more fundamentally, “What turns on the switch?”