Tuesday, October 29, 2013

Chimerism: not being yourself has medical implications

Science has demolished another idea that researchers once knew to be "true" about genes, the chains of molecules that encode the blueprint for the human body. The consensus a few years back was that every cell in each person's body has the same genetic signature, the same set of DNA unique to that person. It is a pretty important concept if you think about it.

Researchers determine things like paternity, genetic risk for disease and presence at crime scenes by examining just a few of the trillion cells in each a person.This practice is based on the assumption that the few cells taken accurately represent the genes in the rest of that individual.

But what if one person had different sets of genes, or genomes, in different cells? Some people, it turns out, have patches of cells with genetic changes in them not found in other parts of their bodies. Some have cells with genes that came from other people.

Such variety is called chimerism or mosaicism, depending on the details, both of which were the subject of a recent article by writer Carl Zimmer in the New York Times. We used the occasion of the article to ask Bruce Korf, M.D., Ph.D., chair of the UAB Department of Genetics, for his thoughts on the implications of these ideas for medicine. 

Show notes for the conference: 

0:35 To recap, the blueprint for the human body is encoded in genes, many of which hold the information necessary for the building of one or more proteins. Gene expression is the process by which information stored in genes is converted into proteins, the workhorse molecules that make up the body’s structures and carry its signals.

1:38 The dogma for decades in genetics was that all cells in one person, having all come from the same original cell (the embryo), had copies of the same genetic material throughout life. That belief was correct to a point, but did not tell the whole story, said Dr. Korf. Each person does indeed have a unique genome, a set of genetic material made up of about 3 billion bases, the “letters” that make up the DNA code, but changes in that code occur every time anyone our trillions of cells divides and multiplies. So mutations are underway constantly, with different changes building up in different groups of cells. Furthermore, several events, some of them more common that once thought, can inject other people's cells into our bodies.

6:35 Chimerism is the presence of two or more genetically different cells occurring in the same body. While we are taught the a fetus results when one sperm fertilizes one egg, more pregnanices than once thought may result from multiple fertilization events. More than one sperm fertilizes more than one egg in the womb get mixed to form one body. Beyond the number of twins born, researchers now suspect that many single baby pregnancies started as twins. One of the embryos then died early on, but not before sharing blood and cells with its twin. Thus you have one baby with the genomes of two babies mixed together. In other cases, two fertilized eggs may fuse together with no evidence they were once two individuals. Obviously, people who get an organ transplant are chimeras as well, as are most mothers, who absorbed their some of their babies' cells while pregnant.

8:15 Chimerism, which happens during conception, is different from the changes in genes that arise from constant small changes in genetic code underway in every human cell over a person's lifetime, a concept called mosaicism. Most of us have patches of cells in our body that have different genes than patches growing elsewhere. While the overall differences are small, mounting evidence suggests they may be meaningful. In the UAB Medical Genomics lab led by Dr. Korf,  the team studies many genetic orders that proceed from mosaicism. In many cases, a patient will have a genetic change that has caused cancer just in one patch of skin, instead of a change across the entire body.

11:06  When a person has two sets of different DNA in their cells, one set will greatly predominate with the other in relatively few cells. Until recently, DNA technologies often could not capture the less frequently occurring genome, losing it in the vast background of the majority. Next-generation sequencing technologies, however, can now identify rare cells that have a different genotype than most of the cells in a person, a capability which may explain why this topic has been more in the news lately. According to the Times article, recent cases have featured genetic test results that found a mother was not the mother of one of her children, and that a sexual assault suspect did not have the same genetic signature in his sperm as in his saliva. The fact both were chimeras threw the tests off.

12:56 While we don't yet know whether cells with different DNA have a big impact on say hearth disease risk, they are known to have a profound role in cancer. Whether the DNA is atypical from chimerism or mosaicism, it is possible the change may affect a cell's ability to divide and multiply, perhaps leading to abnormal growth. Cancer is a disease of mosaicism, said Dr. Korf, because a cell comes to include a small changes in its DNA that remove normal growth limits to create tumors.

16:45  We don't really know how many different genomes we have in the cells in our body. If you look at it one way, we have as many different sets of genetic material as we have cells, since small, unique and random changes slip in as each cell divides and multiplies into two more. Most of the changes have no impact on healthy function, but some do, and the trick is to pick out trillions the few that do.

17:22  Cells with slightly different DNA sequences obviously play a role in cancer, but the remaining question is whether or not small numbers of cells with differing genomes different play a role in other major diseases, like heart disease or Alzheimer's. Is it possible that chimerism or mosaicism in the heart can cause rhythm disorders or that such changes in the pancreas bring about diabetes?

Thursday, October 10, 2013

Goal of next massive decades-long cancer study: reduce cancer to a nuisance

Before the first cancer prevention studies run by the American Cancer Society between 1952 to 1955, and again between 1959 and 1972, Americans had no idea that smoking causes cancer. Before the Cancer Prevention Study II, which started in 1982, physicians and patients didn't fully understand the link between nutrition, obesity and cancer.

The University of Alabama at Birmingham just became the largest enrolling center in the next study in this series, Cancer Prevention Study-3, or CPS-3, with a record 1,209 people signed up to participate at UAB. Nationally, the study will follow the health of 300,000 people for decades in hopes of making the next great leap in the understanding of what causes cancer.

Specifically, the study will track the lifestyle, environments, diet and genetics of people not previously diagnosed with cancer in hopes of understanding what causes or prevents cancer for each person in the coming decades. The ultimate goal is to turn cancer from a major killer into a manageable, chronic disease (a nuisance) or stop it before it starts.

We thought to ask Edward Partridge, M.D., director of the UAB Comprehensive Cancer Center, about the science behind massive, long-term studies like CPS-3, and about why they reveal clues about diseases that other studies miss. 

Show notes for the podcast:

1:06 Population-based studies like this are especially important because they enroll large numbers of people who are well at the beginning of study. Researchers can they see who gets sick over time, and go back to indetify which factors were associated most closely with disease. Sadly, a good many of the people in the study will develop cancer in the coming years, Dr. Patridge said. Was it a certain kind of food, or a certain certain of a gene that created risk? This is a different type of approach than studies that look at whether a drug will work in people who are already sick.

3:14 Massive, decades-long studies reveal patterns where other studies cannot because of the detailed tracking of so people and so many factors for so long. In addition, what the study designers decide to track in each patient is based on many studies in recent years that offered new clues about what to track. Participants take an original survey, which includes trying to recall what their lifestyle was like in their youth, and then repeat the survey every two years. The first of the CPS-3 study results might come out within a year, with more results will then continuing to come out for decades.

4:38 Importantly, this is the first large cancer prevention study that is taking a blood sample from every participant. That will enable researchers to study genetic factors, and their combination of withf other diseases, medications taken. diet, etc., over time.  The research team will also be able to look at epigenetics, the small chemical changes that turn genes on or off in reaction to the environment. In the future, this may enable the field to recognize future cancer risk from a blood sample taken from a perfectly healthy person and in time to intervene.

6:09  The CPS study before the current one, CPS II, led to a publication in 2001 that found obesity to be a major contributor to cancer. Today, some make the arugment that obesity has overtaken tabacco as the major cause of cancer.  In 1970, four percent of children between the ages of six and eleven were obese. Today, that number is 20 percent, a five-fold increase. Children who are obese are much more likely to become obese adults, and public health experts fear that a wave of obesity-related cancer is on its way. CPS-3 will include the largest percentage of obese people of any cancer prevention study so far, and the obesity-cancer link will be closely tracked. 

7:41 Other burning questions in cancer research that CPS-3 will help to answer are, for instance, what is the molecular basis of the increase in cancer risk related to obesity. Researchers will also be looking at what the drop in smoking has meant in terms of reduced risk. Researchers are also keen to study for the first time many of the pharmacuetical drugs taken now taken by so many Americans for large portions of their lives. For instance, what are the long-term effects of a drug like metformin, taken for Type 2 diabetes, on cancer risk?  It may actually reduce cancer risk and the study may explain why. 

9:23 Among the most exciting things about the study is the combination of taking blood samples and the fact that researchers have now mapped the human genome, the complete set of genetic material. That will enable researchers to see which deviations from normal genes are associated with cancer. Dr. Partridge said that he believes this study, and related efforts worldwide, will have eliminated cancer as a major public health threat half-way through the study, say by the year 2050.  By then, the field will detect and eliminate cancers before they become a health threat, or will be turning them into a chronic, manageable conditions, the way drug cocktials have enabled many AIDS patients to live normal lifespans. 

12:19  In a sign of the challenges involved in curing cancer, our society has not yet fully made use of the knowledge and data collected by cancer prevention studies that finished up decades ago, said Dr. Partridge. We all know that smoking causes cancer, and yet 22 percent of Americans still smoke, and even more Alabama. We know that colorectal cancer and mammography saves lives, and yet 40 percent of people with insurance don't opt for these tests. The new study will reveal many insights as well, but making the cultural changes needed to realize their value will be a larger task.

13:45 The fact that so many enrolled locally here in Birmingham says great things about the community, Dr. Partridge said.  He found it particularly gratifying that so many UAB employees enrolled. UAB is a major employer here, and to see nurses, staff, physicians and researchers, many of whom conduct research for a living, becoming participants in research.

14:54 Local enrollment in CPS-3 is closed, but folks can still visit the CPS-3 website to see what the 
nearest enrolling center is. The study will finish up enrolling nationally by December 2013.