Thursday, November 29, 2012

Gut bugs' relationship with estrogen-related cancer

The human microbiome made news earlier this year when the Human Microbiome Project reported its first results on the typical set of microbes living on and in the average, healthy American. It's still in the news because researchers keep finding new ways in which our bacteria, viruses and fungi interact with our bodies to drive disease risk.

Along those lines, the subject of today's podcast is the emerging evidence that each woman's particular set of gut bacteria may influence how she processes the hormone estrogen. One theory holds that some bug species produce enzymes that increase a woman's lifetime estrogen exposure, and potentially, her risk for estrogen-related cancers.  

Talking on that theme in today's podcast is Claudia Plottel, M.D., clinical associate professor of Medicine in the New York University School of Medicine. She is an expert on the "estrobolome,"  the complete set of bacterial genes that code for enzymes capable of metabolizing estrogens within the human intestine. Her interview is the latest in a series recorded recently at a "cancer and the microbiome" research retreat held by the UAB Comprehensive Cancer Center

Shownotes for the podcast

1:00 Trillions of microbes, an immense community, live inside the human body and on its surfaces, interacting with the body to either help or harm it.

1:55 As a medical doctor who treats patients, Plottel has a unique perspective on microbiome research, and on how it may factor into patient care. Interacting with patients gives her a context to ask questions about the microbiome, while her research into the microbiome has made her more aware that any therapy is treating both the human body and its bacteria.

2:30 Beyond probiotics, there are few clinical treatments available that address a person's microbiome on the way to treating their disease, but several are on the horizon. For instance, approaches are under development that promise to restore a healthy population of microbes in a person, or even transplant them from a healthy person.

3:20 A major focus of Plottel's research is the interaction between each woman's gut microbiome and the hormone estrogen. It has been long known that estrogen, a vital hormone for human health, is processed in the liver, and that some of it enters the gut, where it interacts with each person's unique microbial community.

3:42 Also well established is that some of the estrogen entering the gut is recirculated through the body, while the rest of it is excreted. Evidence suggests that each person's mix of gut bugs determines how much estrogen is recirculated, making the microbiome a key regulator of each person's circulating estrogen levels over time.

4:27 Researchers know from studying large groups of women that the occurrence of certain cancers is estrogen-related, and that the incidence of these cancer types varies greatly across the globe. Microbial populations vary along with estrogen-related cancer rates, and projects under way in Plottel's lab seek to determine whether or not the two are linked.

5:22 One enzyme produced by certain bacteria, beta glucuronidase, is present in the guts of about 44 percent of women with healthy estrogen metabolism, so the thought is it plays a major role.

6:08 It has been established that antibiotic treatments change the make-up of the gut microbiome, and that it takes time for the community of helpful bacteria to recover after treatment. Some theorize that antibiotics throw off bacterial regulation of estrogen, and Plottel's team is currently running experiments to see if this is the case.

7:03 Plottel hypothesizes that women who happen to have gut bacteria with stronger or weaker enzyme function may have have higher or lower levels of re-circulated estrogens over their lifetimes, which in turn represents higher or lower risk for certain types of cancers. If this proves to be the case, researchers may be able to use prebiotics and probiotics to reduce risk.

9:00 Estrogen and cholesterol are chemical relatives, and some theorize that obesity, higher blood cholesterol, changes in gut bug profiles and higher risk for estrogen-based cancers are all related. In studies in mice, Plottel observed that antibiotic treatment that changes estrogen metabolism causes the mice to gain weight. Studies in women have also shown that obesity is a risk factor for estrogen-related cancers such as those occurring in the lining of the uterus (endometrial cancer) and in post-menopausal breast cancer. Plottel and others are working now to untangle these many threads.

10:10 The field of microbiome research is exploding in part thanks to the availability of new computational tools that can deal with its complexity, says Plottel. Most of the bacteria making up the estrobolome cannot be grown in culture for study by standard methods, so researchers must rely on genomic technologies and methods that have only become available in recent years.

10:58 Researchers need to look at cancer differently in the context of the microbiome, says Plottel. They should be looking more closely at the organ in which cancers occur, and seeking to determine if the microbial community specific to that organ is playing a role in cancer development.

Friday, November 23, 2012

Next gen sequencing a lens on bug-driven cancer risk

The bacteria, viruses and fungi living on our skin, up our noses and in our guts have a profound impact on our chances for developing cancer and other inflammatory diseases. Every one of the many millions of individual bacteria in our gut, for instance, contains genes that serve as instructions for the building of proteins. These molecules constantly interact with our own cells, helping to do everything from digest food to mistakenly triggering immune responses linked to cancer risk.

With these interactions in mind, the UAB Comprehensive Cancer Center chose "cancer and the microbiome" as the theme for its recent research retreat. The Mix interviewed several retreat presenters, each a nationally recognized expert in the area, and is featuring the chats as a podcast series over the next few weeks.

Our guest today is Michael Crowley, Ph.D., director of the sequencing operations in the genomics core within UAB's Heflin Center for Genomic Science. Before researchers can understand how our complex microbial communities either help or harm us, Crowley says, they must determine which species are present and what they are up to. Much can be revealed by determining the makeup of microbial genes, which offer clues to the molecules and chemicals they release into our bodies, with the help of high-speed sequencing and genotyping tools.

Show notes for the podcast:  

2:15 Fred Sanger came up with the first technique for determining the sequence of the coding units making up human DNA in 1977, and while it has undergone changes, its chemistry is basically the same today, says Crowley.  The technique reveals the order in which the DNA units, or nucleotides, line up to serve as coded instructions for the building of a human being. Initially, the scientists could sequence just a few nucleotides at a time, and then a few hundred. With advances in next-gen sequencing technologies, researchers can now sequence the entire set of genetic information for a person, three billion coding units, in 10 days for $5,000. In way of contrast, it took the Human Genome Project roughly $3.8 billion and six years to do the same thing 10 years ago.

3:47 Crowley is an expert in next-gen sequencing, which analyzes a great many small pieces of DNA in one area all at once on a glass slide. It's like looking at the night sky, seeing all the stars at once, and keeping track of which stars are changing.

4:36 Crowley's next-gen sequencing operation at the Heflin Center is mostly concerned with analyzing genetic material collected from patient samples. The information currently gives researchers clues to how diseases and medications change the microbiome, but in the future, the data will help clinicians adjust care and treatment.

6:11 The most important tool in microbiome and genome sequencing, says Crowley, comes from a company called Illumina, and is called the Genome Analyzer 2X. This second-generation tool enables the team to sequence 95 billion base pairs of information at one time from hundreds of microbiome samples on a single glass slide.

6:33 The question to be answered by this type of analysis changes with researcher that comes in seeking Crowley's help with a microbiome sequence. Often the question is "how has a patient's microbiome changed as he or she developed a disease, or what changes has chemotherapy made in a person's microbiome?"

7:46 Crowley's lab has assisted researchers conducting genomewide association studies, a type of analysis made possible in recent years by the availability of computing power and high-speed sequencing technologies. Such studies compare the genetic makeup of a patients with and without a disease. They determine the variations present at each spot in the genetic code for each person and the degree to which any variation contributes to disease. Crowley's team can look, in real time, at up to five million of these variations, called single nucleotide polymorphisms, or SNPs, which are different for each individual and can be associated with particular diseases.

8:39 The problem with GWAS studies is that they only show that one trait is somehow linked to a disease, not whether or not one can cause the other. Furthermore, associations from GWAS studies can only account for about 5 to 10 percent of the risk of inheriting many diseases. This has been termed the problem of "missing heritability."

8:59 To find this missing genetic risk, the NIH funded the ENCODE project, which has linked diseases to areas of the genetic code, not just to specific genes. The ENCODE project picked up where the Human Genome Project left off in 2003, seeking to understand which bits of the genome have an active role in human biology despite not being genes. While the 20,000 or genes discovered during the Human Genome Project are a central part of the “blueprint for human biology,” ENCODE has helped to confirm that genes represent less than 2 percent of the genome. Genes, it turns out, are surrounded by vast stretches of code, some of which control when, where and how genes turn on and off. Problems with such regulatory sequences have now been implicated in many diseases.

11:36 Sequencing operations in the genomics core within UAB's Heflin Center for Genomic Science work closely with the UAB Microbiome Core in a model where researchers grounded in many disease areas can gain unfettered access to next-gen sequencing expertise and instruments.

13:10 For those interested in reading more on microbiomic genetics, Crowley recommends the NIH's Human Microbiome Project and the National Human Genome Research Institute websites. He also recommends searching Google, which turns up articles including In Good Health? Thank Your 100 Trillion Bacteria (New York Times, @ginakolata), Finally, A Map Of All The Microbes On Your Body (National Public Radio, @robsteinnews) and Discover the Frenemy Within (Wall Street Journal, @ronwinslow).

Thursday, November 15, 2012

Massive computing power needed to unravel gut bug/cancer link

The human microbiome - the bacteria, viruses and fungi living on and in us - made news in June when the Human Microbiome Project first cataloged the mix of bugs for a healthy American.

With the typical set of bugs now outlined, researchers are searching for the bug profiles that correlate with diseases. New understanding of our complex microbial communities is laying the foundation for advances in the treatment of infectious, autoimmune and inflammatory diseases, including the process by which inflammation contributes to cancer.

Against this backdrop, the UAB Comprehensive Cancer Center chose "cancer and the microbiome" as the theme for its recent research retreat. The Mix interviewed several retreat presenters will be featuring the chats as a podcast series over the next few weeks.

Our guest today is bioinformatics expert Elliot Lefkowitz, Ph.D., associate professor in the UAB Department of Microbiology. We talked about how efforts to integrate research on cancer and the microbiome depend on bioinformatics, the high-powered computational analysis needed to reveal patterns within the mountains of data generated around the human microbiome. The data sets involved are many, many times larger than even the three billion coding units making up human genetic material.

Show notes for the podcast:

2:14  Researchers estimate that about 100 trillion microbes live on and in the human body, ten times as many as there are cells in the human body.

2:37  Research on the microbiome is revealing that, along with efforts by the human immune system to keep disease-causing microbes (e.g. bacteria) in check, certain sets of bugs in our body also help to defend against their pathogenic brethren.

3:11 Making matters more complex, the human microbiome is in flux, so it may change from a helpful mix of bugs to one that contributes to disease with changing circumstances. Being able to watch for that profile change would represent a medical advance. This change may be driven by a disease process, or may cause it in some cases.

3:33 The UAB cancer center is interested in changes in the microbiome because evidence suggests that bug profiles are changed by, and may change, cancer processes.

3:53 Bioinformatics is the computational analysis of biological data. Frequently, it deals with genetic sequence information, the DNA coding units that make up the genetic instructions for the building of a human. The order, or sequence, in which those units occur with DNA chains makes up the letters and words in these instructions. They are translated under the right circumstances into the proteins and regulatory elements that make up the body's structures and carry its messages.

4:30 After Michael Crowley, Ph.D., and his team at UAB's Heflin Center for Genomic Science, determine the sequences of the DNA chains in the bug genetic material, Eliott Lefkowitz, Ph.D., and his team at UAB's Molecular and Genetic Bioinformatics Facilty use bioinformatics to analyze them in different ways.

5:05  When Lefkowitz started in bioinformatics 25 years ago, the field was engaged in determining the sequence of a single gene, perhaps made up of about 1,000 coding units, otherwise known as codons.  It was a challenge with the computers of the day, but they did it. A few years later, Lefkowitz and others began looking at viral DNA sequences, which required them to analyze perhaps 200,000 coding units, and then bacteria, with perhaps 2 million coding units in play. With modern day next-gen sequencing, researchers may have to analyze 20 billion genetic units per sample.

7:11 The amount of information that researchers are having to analyze is so overwhelmingly greater that it was even five years ago that bioinformatics experts like Lefkowitz, even with leaps in computing technology, are having to create new computational techniques for using that computing power to get the job done.

8:20 For years, bioinformatics experts, including some at UAB, having been experimenting with concepts like cloud computing and Web 3.0, techie terms for massive stores of patient data and a unified system to analyze it. Lefkowitz and his colleagues work closely with the UAB Information Technology's Research Computing group (UAB ITRC), which makes available to research groups many resources, including the Cheaha cluster. It's a private network of individual data processors networked together to act like a supercomputer. When they need even more computing power, they turn to the cloud, in some ways like the networks that make Google searches so powerful.

10:00 To understand the impact of any individual's microbiome on that person's health, researchers need to know its make-up, the number of each kind of bug in comparison with others present, and what those ratios look like in a healthy person. A healthy microbiome is likely to vary by where you live, but there are some constants that could then be compared against those who have any particular disease.

10:58 Bioinformatics tools make it possible for researcher to compare the numbers and types of microbes in people who are healthy against those with each disease to see if different bugs dominate in people with a disease. Statistical associations promise to yield give clues that may lead researchers to create treatments that change microbes, rather than human cell signalling pathways, to treat human diseases.

13:00 Proteins, the workhorse molecules of human tissue, are made up of functional building blocks, many of which are used again and again by many different proteins. So when researchers see one of the known blocks in a protein of unknown function, it gives them some clues about what it does, especially when combined with bioinformatic analysis. Discovery of such repeating pattern often provides clues to overall biology.

14:20  In analyzing microbial communities, finding repeating patterns, like distribution of each bacterial types, and the ratios of one to the others represent patterns that can be compared between a person who is healthy and another with diabetes, for example. Lefkowitz can go even deeper and look at how at patterns in the proteins created by each set of microbes to see which are associated with disease or health.

Monday, November 12, 2012

Do gut bugs drive cancer risk?

So far, 2012 has been the year of the human microbiome. That's the set of bacteria, viruses and fungi living on our skin, up our noses and in our mouths and guts. The subject made national news in June when the Human Microbiome Project, a massive, NIH-funded effort to catalog the mix of bugs living on and in Americans, reported its first results.

Our ancestors first “invited in” gut bugs, for instance, 450 million years ago because doing so let them harness bacterial enzymes to get more energy from more kinds of food. Today, microbes contribute 360 times as many genes responsible for the human ability to convert food into energy as human genes themselves. Humans and their bugs may now represent a single super-organism.

With the typical set of bugs now outlined, researchers are searching for the bug profiles that correlate with diseases. New understanding of our complex microbial communities is laying the foundation for advances in the treatment of infectious, autoimmune and inflammatory diseases, including the process by which inflammation contributes to cancer. The work could even make possible prescription fecal transplants that replace disease-causing microbiomes.

Against this backdrop, the UAB Comprehensive Cancer Center chose "cancer and the microbiome" as the theme for its recent research retreat. The Mix interviewed several retreat presenters, each a nationally recognized expert in the area, and will feature the chats as a podcast series over the next few weeks.

Our guest today is Casey Morrow, Ph.D., professor in the UAB Department of Cell, Developmental and Integrative Biology and the retreat’s organizer.

Show notes from the podcast: 

0:45 We would be unable to digest most of our food without our microbiome — and it may have helped to establish our immune system. The wrong bugs, though — or our immune system’s reaction to them — also help to drive many infectious and inflammatory diseases, possibly including heart disease and cancer.

1:25 The microbiome is a name for the complex communities of microbes found on and in the various habitats around the body. Over the last 10 years, the field has found that a person's mix of bugs can be extremely helpful or dangerous to them.

2:24 Human microbes have become a subject of greater interest with the realization that we exist in symbiosis with them; that they are a part of us.

2:57 Along with aiding in the digestion of food, these bacteria, viruses and fungi have a complex and ancient relationship with our immune system. In one sense, they teach our immune system how to tell the difference between helpful and destructive bugs, and whether or not to ramp up an immune response. The latter is a crucial decision, because immune responses fight disease in the right context, but they also cause unwanted inflammation when they misfire.

3:12 The field has come to recognize that inflammation caused by an overactive immune system, sometimes in reaction to helpful gut bacteria, contributes to a variety of diseases, including cancer. Beyond triggering immune responses out of turn, some bugs may also release compounds themselves that damage DNA and contribute to cancer risk.

4:16 The team organized this retreat based on the UAB Cancer Center's strategic plan, which reflects work in many labs showing that a person's bug profile not only contributes to inflammation, cancer and obesity, but that all of them influence each other.

5:19 Dr. Morrow and colleagues established a UAB Microbiome Core within the Cancer Center with the help of Cancer Center director Edward Partridge, M.D., but the core is in the process of expanding into a university-wide effort.

6:42 The core is set up such that UAB researchers can easily add microbiome analysis to their ongoing studies of many diseases with a "one-stop shopping" approach. Researchers can bring in samples of microbes from mouths, guts or other habitats in patients or study animals, and the team will analyze the microbiomes. After core scientists prepare the DNA for the client, they hand it off to Michael Crowley, Ph.D., and his team at UAB's Heflin Center for Genomic Science. These researchers determine the sequences of the DNA chains in the bug genetic material, and then send the vast amounts of genetic data they generate through high-speed sequencing techniques to Eliott Lefkowitz, Ph.D., who leads UAB's Molecular and Genetic Bioinformatics Facilty. His team then provides the client with the identities of the bugs in the sample.

8:19 As they conduct clinical trials, researchers interested in diabetes, cancer and obesity can collect samples, store them for later analysis with the microbiome core, and look for associations between microbiomes and pathology. Such analyses promise to help track microbial communities in a given person as he or she goes from health to any given disease state.

9:43 The consensus now is that microbial communities are actively driving health and disease. We even have currently available cultures, yogurts and pills that change the microbiome in the mouth or gut to improve health, part of a billion-dollar industry.

11:25 Presenters at the UAB symposium were among the pioneers that showed the differences between the gut microbiomes of obese and thin people. The UAB microbiome core works closely with UAB's Gnotobiotic and Genetically Engineered Mouse Core, led by Casey Weaver, M.D. Gnotobiotic mice are genetically engineered and raised to have no gut microbiome, and fascinatingly, can be made to gain significant weight if the microbial gut community from an obese human is transplanted into them.

12:29 The gnotobiotic facility offers a system for studying how you can transplant microbiomes from healthy individuals to obese ones, which becomes vital when the goal is to perform such transplants in humans a few years down the road.

Thursday, November 8, 2012

Immunogenomics: more powerful the more it's used

Here we present the fifth and final interview in our podcast series focused on immunogenomics, a field that is using new genomics tools to unravel the complexity of the human immune system and related diseases.

We recorded interviews with experts on the subject from UAB, Harvard, Stanford and the National Institutes of Health at a recent immunogenomics symposium organized jointly by the HudsonAlpha Institute for Biotechnology and leading medical journal Nature Immunology. The symposium was sponsored in part by UAB and its Center for Clinical and Translational Science.

Our guest for this podcast is John O’Shea, M.D., scientific director of the National Institute of Arthritis and Musculoskeletal and Skin Diseases, and chief of the NIAMS Molecular Immunology and Inflammation Branch.

We talked about how immunogenomics will only achieve its potential when its tools become inexpensive and straight-forward enough that they can be folded into research efforts by non-genomics experts. O'Shea said early examples of that could be found in the symposium presentations, some of which provided insight into how the immune system drives disease while others predicted which patients should benefit most from new classes of drugs.

Show notes for the interview

1:01 Those who study the immune system have also closely studied genomics for years. What has changed in immunogenomics is the leaps made possible by new technologies. Immunologists now have the ability, given cheap, powerful tools, to conduct genomics studies as part of their research.

2:31 High-powered gene sequencing, bioinformatics and computing tools will only become truly powerful when immunologists, cardiologists and neurologists (non-genomics experts) start using them in their labs worldwide. Many presentations at the symposium represent examples of that starting to happen.

2:57 O'Shea's lab, which was a pure immunology lab five years ago, now includes several high-throughput sequencing machines, not to mention a dedicated computational biologist. Immunogenomics is changing the makeup of the average research lab.

3:34 Immunogenomics is important to O'Shea's research in particular because he works with immune cell signalling pathways that play a central role in autoimmune diseases like rheumatoid arthritis, where the immune system mistakenly targets and damages our own cells. It provides a whole new window on related mechanisms if you can understand which small variations in certain spots within our genetic code add risk for the disease.

4:03 Specifically, Dr. O'Shea is interested in immune signaling chemicals called cytokines that ramp up our immune response to infectious disease invaders, but that also trigger inappropriate immune reactions as part of autoimmune disease. Genomics tools helped the field determine that a certain cytokine signaling cascade called the JAK-STAT pathway was centrally involved in autoimmune disease. Now we know that small genetic changes, so-called polymorphisms, in STAT molecules confer risk for rheumotoid arthritis, lupus, Sjogren's syndrome, etc.

5:29 Interestingly, as the field tries to figure out what confers disease risk relative to the JAK-STAT pathway, a new class of drugs, the JAK inhibitors, are arriving on the scene. Some are under consideration for marketing approval at the U.S. Food and Drug Administration right now. With this arrival, new immunogenomics tools will help researchers understand which patients are more likely to respond to the new drugs, saving them time and misery.

6:08  O'Shea's presentation at the meeting was titled "Environmental Sensors and Master Regulators in the Emergence of Active Enhancer Landscapes." Put simply, all cells in a person have the same DNA, but all cells don't read the same sections of the instruction encoded in that DNA. To fulfill its specific functions, each cell reads certain parts of the same code, with mechanisms in place to open and close the right sections of the book. The mechanisms that control when genes are expressed are regulatory sequences, the subject of study in the science of epigenetics.

7:20 An increasingly popular theory is that the origin of many diseases, including autoimmune diseases, lies not with genes, but instead within the small pieces of epigenetic code, the enhancers and regulators, that control the process of when and where genes are turned on.

9:21 Genomics and epigenomics, the genetic cards we are dealt, have a great deal to do with our risk for disease, but our "environment" plays a big role as well. Environment in this context could mean sunlight, hormonal changes (estrogen versus testosterone), or how much inflammation a person has thanks to chronic disease. The excitement is around our new ability to measure the interplay between genetics and these other factors in disease risk using the new tools.

11:40 Over time, O'Shea and others have switched from using technologies that examine a single gene, to a few genes, and now, all human genes at once, the analysis of 3 billion coding units. As a result, many diseases are now known to be the result of changes in large networks of genes.

14;19 For more information on where immunogenomics meets epigenetics, O'Shea recommends the Nature website covering the ENCODE project, the NIH-funded effort to begin to map the regulatory portions of the human genetic code.