Immunogenomics advances point to new biomarkers, therapies

Next-generation gene-sequencing technology and new data-analysis tools are pointing the way to fresh diagnostic and treatment approaches for autoimmune diseases, cancer and many other conditions. That was the message at Immunogenomics 2014, a recent conference hosted by Huntsville’s HudsonAlpha Institute for Biotechnology and Science magazine for researchers studying the interaction between genes and the immune system. The event was sponsored in partnership with UAB and its Comprehensive Arthritis, Musculoskeletal and Autoimmunity Center (CAMAC).

Investigators from major national and international research institutions described how detailed profiles of immune cells could improve response to influenza vaccines and accelerate new treatments for emerging infectious diseases. They explained new immune-mediated links between microbial populations and cancer risk, and highlighted progress in understanding the pathogenesis of complex diseases such as multiple sclerosis.

“We now have the tools to examine these gene-disease associations in finer detail,” said S. Louis Bridges Jr., M.D., Ph.D., director of UAB’s Division of Clinical Immunology and Rheumatology and the CAMAC. Bridges is using genomic techniques to study the autoimmune condition rheumatoid arthritis. Bridges presented his research at Immunogenomics 2014, and served as chair of a session on the genetics of complex disease. “We’ve started to refine our analysis to home in on cells with an increasing degree of specificity,” Bridges said. “Technology is now allowing us to analyze in more detail specific subsets of cells, including ultimately at the single-cell level.”

From Associations to Biomarkers

Genomewide association studies have identified a host of genetic changes linked with disease. “Now investigators are looking at the functional effects of these polymorphisms,” Bridges said. “It could be that a polymorphism affects expression of a certain gene, or it may only affect expression of that gene in a certain cell type.” Bridges’ project, being performed in collaboration with UAB epidemiology chair Donna Arnett, Ph.D., and HudsonAlpha investigator Devin Absher, Ph.D., is examining genetic risk factors in African-Americans with RA.

"We now have the tools to examine these gene-disease associations in finer detail," Bridges said. "We've started to refine our analysis to home in on cells with an increasing degree of specificity."

In his talk at Immunogenomics 2014, Bridges demonstrated that overexpression of the interferon gamma 2 receptor gene is strongly linked with severity of disease in African-American patients with RA. “Our next step is to see in which cells that particular expression occurs,” Bridges said. This work could ultimately point the way to biomarkers that tell clinicians which of several known signaling pathways is active in a patient with RA, guiding treatment decisions.

Epigenetics and Therapeutics

Researchers are also focusing increasing attention on the ways gene expression is regulated dynamically in cells through epigenetic changes, says Robert P. Kimberly, M.D., director of the UAB Center for Clinical and Translational Science. Epigenetics refers to mechanisms that alter gene expression without changes in the actual DNA sequence. One of the most common epigenetic changes is methylation. When a methyl group attaches to the DNA base cytosine, it blocks the ability of the neighboring gene to be expressed.

Tracking and analyzing epigenetic markers implicated in a particular disease — such as systemic lupus erythematosus, one of Kimberly’s own research interests — could give clinicians crucial information on “if to treat, when to treat and also how to treat” that condition, he said.

For example, if a key risk gene is hypo-methylated in a patient — increasing the likelihood of the gene’s being expressed — “that could mean the patient is poised for a flare-up of disease,” Kimberly said. Another patient, who would look exactly the same to a clinician, would be much less likely to have a flare-up if that gene is hyper-methylated, he adds. “Understanding this epigenetic regulation, and eventually manipulating it to therapeutic advantage, is very exciting.” This research is a focus of several investigative teams at UAB, Kimberly says.

A “tree map” depicting the immune diversity in a patient diagnosed with Parkinson’s disease. Each rectangle represents a unique antigen receptor detected in the sample, and the size of each rectangle represents the relative frequency of that receptor within the sample. (Color is arbitrary.) Image courtesy iRepertoire.

Profiling Immune Signatures

One advance highlighted by several presenters at Immunogenomics 2014 was immune repertoire sequencing. Researchers now understand that an individual’s immune response is based greatly on the specific cell populations, or “repertoire,” present in that individual. For both T and B cells, for example, millions of distinct variants are possible. The exact mix is determined by a person’s encounters with microbes, disease and other environmental exposures over a lifetime, explains HudsonAlpha investigator Jian Han, M.D., Ph.D., a 1991 graduate of UAB’s medical genetics doctoral program.

Everyone produces T cells, for example, Han says. “But which one of those naive T cells gets used is determined by if it met, and was activated by, its antigen.” By analyzing the variety of T and B cells present in a particular patient, or mapping the repertoire commonly found in a particular disease, researchers can identify biomarkers to aid in diagnosis and treatment, Han notes.

Han’s HudsonAlpha lab has pioneered the multiplex PCR technology needed to gather the massive amounts of data required for repertoire sequencing, and the analytical tools required to resolve that data into meaningful reports. His presentation at Immunogenomics 2014 focused on Repertoire10K, a HudsonAlpha-funded project to sequence the immune repertoires of 10,000 patients: 100 with each of 100 critical diseases. The goal is to identify a signature in the immune repertoire for each disease. UAB researchers have been key contributors of the genetic samples that are critical to the project, Han says. In return, the investigators have access to state-of-the-art sequencing data that can advance their own studies.

Team-based Science

Collaborations between investigators at HudsonAlpha and UAB have taken place since the institute first opened in 2008, Kimberly says. But the new UAB–HudsonAlpha Center for Genomic Medicine, launched this summer, will increase these research partnerships and speed new discoveries in immunology, cancer, cardiovascular disease and many other fields, he notes.

Leveraging the strengths of each institution is critical as the scale of the research challenges becomes ever greater, Kimberly adds. “To understand what’s really happening in disease states, we’re going to have to be able to take all the data on genomics, epigenetics and more and figure out how to pull it all together,” he said.

That’s why UAB is also creating a new Informatics Institute. It will work in tandem with the UAB–HudsonAlpha Center for Genomic Medicine and a third initiative, the UAB Personalized Medicine Institute, to build the infrastructure and recruit the data scientists needed to succeed in this new era of research.

“It’s a major frontier right now,” Kimberly said. “The algorithms to combine all this data for the most part haven’t even been formulated yet. But it’s clear that the institutions that succeed in the future will be the innovators in this area.”

Exploring new frontiers in personalized cancer care

Personalized medicine is turning medical care on its head, and cancer treatment is at the forefront of that revolution. The UAB Comprehensive Cancer Center’s 17th Annual Research Retreat introduced this cutting-edge work to an audience of nearly 400 clinicians and researchers. The topic was timely after this summer’s announcement of major initiatives in genomics and personalized medicine at UAB, including a research consortium between the Cancer Center and Huntsville’s HudsonAlpha Institute for Biotechnology.

“Personalized medicine is the future of cancer care,” noted Eddy Yang, M.D., Ph.D., associate professor in the UAB Department of Radiation Oncology, who organized this year’s symposium. “This is certainly a glimpse of what is to come for the Cancer Center and UAB as a whole.”

The Future: Cancer as a Chronic Disease

“Oncology has been a first mover for personalized medicine,” said invited speaker Mark Boguski, M.D., Ph.D., founder of Genome Health Solutions and a faculty member at Harvard Medical School.

Boguski shared his remarkable vision. With the use of personalized medicine, he said, we can now begin to reimagine cancer as a manageable chronic disease. Subsequent speakers amplified that theme, describing advances, challenges and roadblocks to delivering personalized cancer care to patients across the United States.

Boguski began with three patient case histories.

The first was a patient in 2010 with adenocarcinoma that was EGFR-positive (that is, it contained mutations that activated the EGFR pathway). When treatment with the usual drug failed, genomic and transcriptomic analysis showed why — metastases from the original cancer were no longer EGFR-positive. But biomarkers on those cancer cells successfully identified a target for a different drug that was effective.

The second case was a metastatic squamous cell carcinoma. Genomic analysis showed, surprisingly, that it could be treated with a hematological cancer drug.

“You wouldn’t guess to use that on a solid tumor,” Boguski said.

Similarly, in a case of advanced lymphoblastic leukemia, genomic analysis unexpectedly pointed to using a renal cell carcinoma drug. With this sea change in the way that oncologists can make their treatment decisions, cancer patients are beginning to ask that their genomes be analyzed, Boguski said.

The UAB Cancer Center’s Molecular Tumor Board, initiated last year, identifies patients who could benefit from DNA sequencing of their tumors, said Yang. These tests, usually conducted in patients with rare tumors or tumors that do not respond to typical treatment, can identify off-label uses for cancer drugs. For example, BRAF inhibitors, which are approved for melanoma, have been used to treat patients with other tumor types that nevertheless harbor the BRAF V600E mutation, Yang said. In another important consideration, “treating physicians have been successful in getting third-party payers to pay for these drugs outside the ‘approved’ indications using the profiling results,” he explained.

Cancer Center Honors Research Excellence In addition to talks by leading investigators, the Cancer Center’s research retreat also features the work of a new generation of cancer researchers. Graduate students, postdoctoral fellows and junior faculty members took part in the annual poster competition; the 131 presentations emphasize the breadth of studies ongoing in the Cancer Center, from cancer prevention to bioinformatics. See the award winners here.

But roadblocks prevent the widespread delivery of such personalized, targeted care, Boguski noted in his talk, because:

• 80 percent of cancer care is delivered away from the top 50 cancer centers.
• Most doctors suffer from a knowledge gap; they need accelerated genome training to understand the top molecular biomarkers and how these markers can guide patient therapy.
• Pathologists — who are a key link to alter the delivery of care — need to know not only tissue pathology but also how to test for and report the molecular drivers of cancer.

Genomics Identifies Actionable Targets

Mark Kris, M.D., an attending physician at the Memorial Sloan Kettering Cancer Center and professor at the Weill Cornell Medical College, showed how genomics and personalized care can be harnessed to improve lung cancer survival.

Working with 11 cancer centers, Kris and colleagues tested 1,000 patients who had stage IV lung cancer. While tissue pathology confirmed adenocarcinoma, the cancers also underwent mutational analysis to probe for oncogenic drivers, and these findings were shared with physicians.

Two-thirds of the patients had at least one of 10 known oncogenic drivers. These drivers are “actionable targets” that helped to guide treatment choices, leading to increased median survival for these advanced cancer patients.

The French medical system, Kris noted, has provided genotyping to every lung cancer patient since 2011, at a rate of 20,000 patients a year. This equity of access to innovation does not exist in the United States, Kris said, even though the National Comprehensive Cancer Network clinical practice guidelines for non-small-cell lung cancer already list a set of molecular drivers that should be looked to to classify and guide treatment.

Needed: A New Kind of Trial

Another roadblock is the need for new ways to perform clinical trials of investigational drugs, said Donald Berry, Ph.D., professor of biostatistics at the M.D. Anderson Cancer Center and a co-founder of Berry Consultants.

Berry described how the use of Bayesian biostatistics in an adaptive platform trial can lower the numbers of patients needed for the trial, while simultaneously investigating multiple drugs and targets. He focused on a current study, I-SPY2, which is investigating treatments for breast cancer. (Berry noted that UAB is one of the largest contributors of patients to the trial.)

Data obtained during trials such as I-SPY2 are used to guide changes in the studies midstream, Berry explained. The result is nimble, lean studies that yield a more dependable estimate of the chance that a particular drug will succeed in its subsequent Phase III trial. Such information is crucial, given the cost and the failure rates of conventional Phase III trials.

Predicting Patient Response With Avatars

The final outside speaker, Paul Haluska Jr., M.D., Ph.D., associate professor of oncology at the Mayo Clinic, described an “Ovarian Avatar” model to personalize ovarian cancer treatment. The avatar is created by implanting live cancer tissue from the cancer patient into a mouse within two hours of surgery.

Haluska shared several definitions involved in this model:
• “Xenograft” is a tumor taken from one species and implanted in another;
• “Orthotopic” means the implant is placed in the natural body location for that type of tumor;
• “Patient-derived Xenograft” is a direct implant from the patient into the other species, without any intermediate in vitro growth or manipulation; and
• “Avatar” is thus an orthotopic, treatment-naïve, patient-derived xenograft.

Mayo implanted its first model in March 2010. Through this September, 404 models have been injected and 294 of them successfully engrafted. The avatar responses to a drug, Haluska said, appeared to mirror the patient responses to treatment with the same drug, and the avatars are being used for drug development.

The next step will be to actually use a particular patient’s avatar to direct her therapy. “It will be the first ovarian cancer with xenograft-directed therapy,” Haluska said. “The best predictor of response is response.”

Oncogenic Drivers and Racial Disparities

UAB has its own xenografts that are derived from glioblastoma multiforme tumors, said Christopher Willey, M.D., Ph.D., an associate professor in the Department of Radiation Oncology and director of the UAB Kinome Core (pronounced “k-eye-nome”). But these personal avatars have a problem — they take too much time to establish compared to the rapid and fatal course of glioblastomas. So Willey hopes instead to use “kinomic” profiles of established avatars from other patients to guide the treatment for a new patient; glioblastoma tissue removed from the new patient during surgery can quickly be kinomically profiled.

Kinomics uses substrate arrays to identify which kinase enzymes — often found to be key oncogenic drivers — are active in the cancer cells. This can help select among about 30 cancer chemotherapeutic agents that target kinases.

The other UAB speaker, Phillip Buckhaults, Ph.D., associate professor in the UAB Division of Hematology and Oncology, described his search for genetic mechanisms that lead to earlier onset and higher incidence of breast and colon cancers in African-Americans, as compared to Caucasian-Americans. His trail began with the discovery of a point-mutant variant of the TP53 tumor suppressor gene in African-Americans, and it has led to the variant’s effect on the PRDM1 chromatin-silencing gene.

Translating research insights from the laboratory to the clinic is a major focus of the UAB-HudsonAlpha cancer consortium, noted Cancer Center director Edward Partridge, M.D. “We’re not at the point yet where we can routinely apply genomics information from the tumor to treatment; but we’re clearly learning, and learning at a rapid pace,” Partridge said. “The goal of the consortium is to accelerate that, and we’re excited about what it means for the care we can bring to our patients.”

— Jeff Hansen

How do mom's microbes affect pregnancy outcomes? UAB research aims to find out

As a baby slides out of the birth canal, on the way to its first breath, its body becomes coated in its mother’s microbes. This first interaction with outside organisms could be key to shaping the development of the baby’s immune system.

Our microbes, collectively called the microbiome, most often live in harmony with our bodies. They support the immune system, help to digest food and keep the metabolism on track, and fight off disease-causing bacteria. But researchers suspect that mom’s microbiome could play a role in when her children are born, and what happens to them as they grow.

“Most people know about the microbes that colonize the gut,” says Rodney Edwards, M.D., an associate professor in UAB’s Department of Obstetrics and Gynecology. “But there are bugs in and on us in many other sites—our skin, our mouths, our noses, our genitalia.”

During pregnancy, it turns out, the new needs and demands of a woman’s body change the numbers and types of these microbes. Alterations in how the body divvies up nutrients, stores fat, and produces hormones shift the properties of the microbes’ environments. But exactly how the microbiome changes over this nine-month period varies between pregnancies. And these variations, researchers are discovering, could impact not only the well being of a pregnant women herself, but the likelihood of pregnancy complications and the long-term health of a baby.

Epigenetics has impact on health beyond DNA

As a science writer, I struggle to translate complex ideas like genetics into straightforward language.  Having covered genes many times over the years, I have come to depend on a few handy stock sentences that I recycle in story after story:

• 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. 
• Human genetic material includes about 3 billion bases, the “letters” that make up the DNA code containing genetic instructions.

Then about seven years ago, research surfaced that required the crafting of a new group of stand-by sentences. It turned out that, while genes were important, they represented just one part of a more complex human genomic system. Genes, the specific batches of code directly for the construction of proteins, were found to comprise just two percent of human DNA. Then humans were found to have one-fifth as many genes as wheat. What made us so complex then if not our genes alone?

The explanation was that we put the same genes to many uses with the help of complex regulatory mechanisms that govern when, where and to what degree our genetic material is accessed and activated. Some of these functions are performed by myriad non-gene DNA snippets called regulatory elements.

Still other recently discovered mechanisms contribute further to our genetic regulatory finesse, and without changing the instructions encoded in the DNA we get from our parents. Such changes represent the province of the emerging field of epigenetics and the focus of a recent UAB Epigenetics Symposium. The Mix – the UAB research blog – interviewed some of the presenters and is featuring the talks in a series.

Our guest for this podcast is Bruce Korf, M.D., Ph.D., chair of the UAB Department of Genetics, one of the organizers of the symposium.

Show notes from the Podcast:

:40 Epigenetics is defined as changes in human gene expression caused, not by changes in the order of base pair "letters" making up the DNA code (such changes are called mutations), but instead by chemical actions that affect the ability of the instructions encoded in a given stretch of DNA to be read and followed.

1:15  Researchers have long known that changes that turn genes on or off play a critical role in fetal development and in the response of humans to their environment, but not what controls those changes. It's now becoming clear that epigenetic mechanisms can permanently silence a gene, for instance, in a particular cell type.

2:01  Cells divide and multiply as the human fetus develops.  Epigenetic changes do not just turn off a gene at a particular point in time, they turn it off in that cell and in all its descendants. That makes such changes useful a gene needs to be turned off permanently to, not only enable a stem cell to become a brain cell, but also to make it the proper sire of a line of many brain cells. The same genes that got a cell to the right stage in development may need to shut down for it remain the right cell type.

2:18 Methylation, the chemical attachment at a certain point on the DNA chain of a methyl group (one carbon atom bonded to three hydrogen atoms), is a principle type of epigenetic regulatory change.

2:25 Methylation is the attachment of a methyl group to cytosine, one of the four bases that encode genetic instructions with the DNA chain. When the methylation occurs at a cytosine that falls next to a guanine, another of the four bases, the methylation will make it possible for other proteins to bind to the DNA chain such that the surrounding gene is silenced.

2:47 The methylation interferes with a process by which DNA forms a complex with proteins called histones to form chromatin, which in turn makes stretches of DNA available to the gene expression machinery upon receipt of the right signals.

4:11 While we inherit our DNA code from our parents, epigenetic changes are not passed on. When a sperm or egg cell is produced, all the epigenetic marks are wiped clean.  Thus, epigenetic fine-tuning of gene expression begins a anew with each person. Combine this with the fact that sunlight, cigarette smoke and the foods we eat make epigenetic changes, and we all become authors of our own gene code.

4:56  "Superfoods" like broccoli have linked to methylation status, and experiments months in mice have shown that diet can change the methylation status of specific genes (say those involved in cancer risk).    

5:19 An interesting area of research in epigenetics is looking at lifelong risk of certain diseases (like Type 2 diabetes) based on events and influences that occur while that person is still in the womb.

6:18 Dr. Korf said the UAB epigenetics symposium is being held now because recent meetings on the UAB School of Medicine strategic plan revealed that many researchers were working in this area independently, and would benefit from collaborations.

7:35 Among the examples of key epigenetics research efforts underway at UAB, David Sweatt is looking at at the potential role of epigenetic changes in learning and memory, TrygveTollefsboll at fundamental aspects of epigenetic biology and Molly Bray at the impact of epigenetic changes on lifelong obesity risk.

8:00 The field is in its infancy in terms of determining epigenetic changes and what drives them tissue by tissue in conjunction with environmental factors. What is truly exciting now is the emergence of extremely powerful tools, the bioinformatics and high-speed genetic analysis technologies, that are driving the field forward.  There will probably prove to be as many epigenomes as there are tissue types in the body.

9:14 Some of the most exciting near future advances are coming in the epigenetics of cancer.  Mounting evidence suggests that some of the changes that turn genes off contribute to the development of cancers.
Tracking epigenetic changes may have predictive value in looking will benefit from a therapy and who is at risk for a cancer.

9:33 It has now been shown that some drugs interact with epigenetic changes, which raises the possibility of using drugs to turn back on genes silenced by abnormal, epigenetic mechanisms as part of disease.

Evolving in a sea of microbes

2012 was the year of the microbiome, the set of bacteria, viruses and fungi living in our noses, mouths and guts. It made national news in June when the Human Microbiome Project first reported on what the bug mix looks like on and in a typical, healthy American.

New understanding of our 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.

For these reasons the UAB Comprehensive Cancer Center chose "cancer and the microbiome" as the theme for its recent research retreat, and The Mix interviewed retreat presenters for a podcast series.

Today's guest is George Weinstock, Ph.D., professor of Genetics at the Washington University School of Medicine.  We talked about his leadership role in genomics revolution, including his contribution to the design of both the Human Genome Project and the Human Microbiome Project.

Show notes for the podcast

1:12 Our world has been dominated by microorganisms for three billion years. All life then involved in this sea of microbes, and humans are no exception.

1:45  Having evolved in a world awash with microbes, the human body is colonized by specific sets of them that provide us with hundreds of times more functions than our own genes can't deliver. Human cells, for instance, have borrowed signalling pathways from microbes that help us digest our food, protect us from being infection, etc.

2:39 Insects have microbiomes too, they they are much simpler than ours. One related theory is that our immune system is more sophisticated because it had to learn to safely handle the many bugs we "invited" to help us digest our food. Taking the idea a step further, some experts think the immune system’s ability to repel unwelcome invaders might represent a lucky, evolutionary after-effect of its more ancient role — managing a stable of helpful bacteria.

3:58 At the heart of Weinstock's decades-long career is DNA sequencing, the technology that enables researchers to determine the order of DNA coding units as a step toward understanding the function of each DNA snippet. The same methods were used to do this for 25 years, but then in 2006 new methods matured that made possible to vastly accelerate the pace of sequencing.  Weinstock's lab can now do in a day what it once took years to do.  For instance, his team can determine the sequence of several human genomes in a day, each requiring the analysis of 3 billion units of code.

6:06 The new high-speed technologies have made possible massive undertakings in genomics, including the 1,000 Genomes Project, The ENCODE project and the Human Microbiome Project.

7:06 Weinstock is among the pioneers that helped to launch the Humane Genome Project, which ran from 1998 to 2003 and offered the first estimate of the 20,000 or so genes present in the human blueprint. Before that project, he was among the very first to sequence a genome from any creature, in his case the bacteria responsible for causing syphilis.

9:36 Weinstock also helped to organize the Human Microbiome Project, which this summer published a series of reports in Nature and several Public Library of Science journals that revised the understanding of how microbes drive either health or disease. Researchers from 80 institutions spent five years collecting and sequencing samples from 242 healthy volunteers.

11:07 Bugs don't colonize humans one by one, but instead as part of large, complex communities.  They interact so thoroughly with each other and our cells that they must be analyzed together. Newly available technologies made it possible to analyze the genes of thousands of organisms at once, and the National Institutes of Health decided to invest heavily. The goal is to quickly advance the understanding this huge aspect of human health driven by our microbes. The NIH funded several genome centers to sequence bacterial genomes, with Weinstock's lab among them.

11:34 Beyond just looking at bacteria, the project funded a number of clinical researchers to study how each person's microbiome affects everything from acne to urinary tract infections to the risk for inflammatory disease in premature babies to cancer.

12:28  While the NIH did not think the project would instantly cure diseases (the genomics are too complex), they did hope to understand how you study the microbiome and what resources would be required. 

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.

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).

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.

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.

Key to immunogenomics value: embed research in healthcare system

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

We recorded interviews with nationally recognized experts in this area 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 meeting presenter Robert Plenge, M.D., Ph.D., assistant professor of Medicine at Harvard Medical School – and Director of Genetics and Genomics within the Division of Rheumatology, Immunology and Allergy at Brigham and Women’s Hospital.

We discussed how immunogenomics has provided a flood of new clues about the genetic quirks contributing to many diseases, but the field must now, with the quirks as a guide, delve back into cells to learn the details of how such changes cause disease. To do so, they must collect human cells from patients known to have a given disease, and related efforts will accelerated the trend toward "embedded" genomics research.



Show notes for the interview:

1:01 Genomics is the study of DNA, RNA and the proteins that code for and how they contribute to health and disease. Immunology is the study of how several cell types fight infection, and why they attack our own tissues in some case to cause inflammation as part of inflammatory and autoimmune diseases. Immunogenomics then is the study of how these components work together, the genetic programming of the immune cell sets.

1:54 Plenge's work focuses on determining the genetic basis of predisposition for autoimmune diseases, and for rheumatoid arthritis in particular. Past genomic studies have determined some of the genes that contribute risk for rheumatoid arthritis, but immunogenomic studies are going further to determine the effect that genetic variations are having in cells, and at what that says about disease mechanisms.

3:19 The last few years have seen the rise of genome-wide association (GWAS) studies, where researchers use genomic technologies to examine every coding unit in the entire genomes of two sets of people (one with a disease, one without) to reveal every small genetic difference. They use tool called microarrays to look at large numbers of genetic sequences all at once, and to find small variations called single nucleotide polymorphisms (SNPs) associated with any given disease.

3:35 But GWAS studies only show that certain families have certain genetic variations that make them more susceptible to certain disease. They do not tell how or why the variations cause disease.  The next step then for Plenge and others will be to roll up their sleeves, go into the lab with this GWAS information and study the cells of people with disease-causing genetic variations to reveal disease mechanisms that can be countered with precision designed therapies.

4:29 Plenge's presentation talks about the importance of biomarkers, the physical measures that show a disease is underway or that a drug is countering it.. These are the tests that give meaning to clinical trial results. Researchers hope that new biomarkers will help them predict who will respond to a given treatment for rheumatoid arthritis based on their immunogenomic profile.

5:12 Plenge is working with the Pharmacogenomic Research Network (PGRN), organized by the National Heart Lung and Blood Institute, part of the Institutes of Health, to see if genomic patient profiles can be used to predict which patients are likely to respond, for instance, to an important category of treatments for rheumatoid arthritis called anti-TNF biologic drugs.

5: 47 It may be that most clinical trials will soon come to benefit from the addition of immunogenomic tools that predict any given patient's response to treatment, or their likelihood to experience a given complication of side effect.

6:22  It's easy to think of the immune system as involved in fighting infection, or even in autoimmune diseases like rheumatoid arthritis where the system mistakenly recognizes its own tissue as foreign and attacks it. Mounting evidence argues, however, show that "mistakes" by the immune system bring about inflammation at the root of cardiovascular disease, neurodegeneritive conditions, cancer, pulmonary disease, etc. A profound understanding of the interplay between genomics and immunology will offer tremendous opportunities to develop new therapies, says Plenge.

7:25 Immunogenomics may help to lessen the massive time and cost necessary today to conduct the average clinical trial. Plenge hopes that emerging techniques and advances will create efficiencies in medical research.  Treatments that address inflammation in rheumatoid arthritis may also prove to have utility in reducing inflammation contributing to say diseased arteries. The potential for this becomes greater the more profound the field's understanding of genomic/immune system interplay.

9:27 Many of the past studies in immunology and genomics were done in mice meant to serve as models of human disease.  But mice are different than humans. There are now many more opportunities to do what Plenge calls "embedded immunogenomics," where registries collect cells and data from human patients for study as part of routine clinical care.  The research is embedded in the healthcare system. If patients consent for a quick blood draw, researchers gain access to details of subsets of cells and genes linked to diseases, and can follow changes over time.

11:13  One emerging trend may be the uncoupling of such genetic registries from a doctor's office visit. People participating in the new registries may just stop by a lab (e.g. Quest Diagnostics) for testing whenever they don't feel well.

12:20 Plenge recommends that researchers interested in learning more about this area look into a database under development called Immunobase, which is working to catalog inherited genetic variations contributing to a wide variety of diseases. The work underway at Sage Bionetworks and  i2b2 (informatics for integrating biology and the bedside), an NIH-funded biocomputing initiative, represent other interesting initiatives. Patients interested in participating in research might look up 23andMe, and those with rheumatoid arthritis, the Arthritis Internet Registry.

Tune in next Friday to hear our talk with John O’Shea, M.D., chief of the Molecular Immunology and Inflammation Branch with the National Institute of Arthritis and Musculoskeletal and Skin Diseases, part of the National Institutes of Health.

Human immuno-genome interview series: UAB's Casey Weaver

Most of the time The Mix covers general research topics, but for the next several Fridays we will feature a podcast series focused on the emerging field of immunogenomics.

We recorded the interviews live 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.

Immunogenomics as a field is using new genomics tools to unravel the complexity of the human immune system and related diseases, which are now known to include heart disease, neurological disease and cancer because of their interplay with inflammation. The work promises to improve diagnostic tools and offer new treatment approaches.

Among the most important of genomics tools are microarrays, which enable researchers to measure the expression levels of many genes at once, and bioinformatic programs, which identify patterns in the massive data sets generated during genomic analysis of individuals and populations.

Our guest for this podcast is meeting presenter Casey Weaver, M.D. professor in the Department of Pathology within the UAB School of Medicine. We discussed how immunogenomic tools have helped researchers to finally grapple with and begin to dissect the complex workings of the immune system, and specifically, of T cells.


Show notes from the podcast:

:57 Our view off the immune system has been zooming in for years, from early studies that looked at the system at the cellular level, to studies that examined the relevant molecules inside cells, and now, to studies looking at the genes that control it.

2:00 Weaver's team has been trying to understand how T cells, one of the workhorse cell types of the precise, thorough and massive adaptive immune response, are controlled by genes that code for cytokines, signaling proteins that ramp the immune response up and down as needed. The team is also interested in the process by which more stem-cell-like T cells "decide" to become one of several more specialized cells, depending on the kind of bodily invader encountered.

2:24 CD4+ T cells are the "master regulators" of the immune response, and Weaver studies how these cells decide to mature into different types of immune cells depending on the kind of immune response needed. His work in recent years has been aimed at mapping the genes expressed in each scenario.

2:45 Weaver's team is working to genetically engineer mice in which researchers can see a readout of which genes are expressed in which immune cells and when. It has became clear how limited the current understanding is of how immune genes are controlled in T cells.

4:13 Every kind of microbial challenge (virus, bacterium, fungus) requires a different kind of immune response to eliminate it. CD4+ T cells differentiation adapts to each threat, matching up with so that it can oversee the right response.

5:11 Along with genes controlling T cell responses, there are often small pieces of genetic material that regulate when and where genes turn and of.  Weaver's team has spent time identifying several of the regulatory genetic elements that control T cell cytokine genes. Several of these elements are cis (lie alonside) the genes they control.  

5:51 Rapid advances in genomic data and technology have enabled researchers to establish correlations between small changes in genes, and in the regulatory elements that govern them, and susceptibility for many diseases.

6:19 How susceptible a given person is to an immune-mediated diseases may depend on small changes in certain genes, so-called single nucleotide polymorphisms or SNPs, but the field is not sure of their data.  Does a certain SNP cause disease, or is it just in the same region as something else that does?

6:59 One way to answer that question is to test the impact of a SNP in a live organism where the immune system is at work. Part of the strategy in Weaver's lab then has been to put part of a human cytokine gene with a SNP associated with a disease into a mouse model, and to see if it has the predicted impact.

8:15 Part of the difficulty of analyzing gene expression traditionally has been that transgenic techniques (putting human genes in a mouse) may end up putting that gene into the mouse genome in several places and randomly.  That makes it hard to pick up the subtle readouts you need to tell whether or not a SNP is contributing to a disease. Weaver's solution, one used by other labs as well, is to insert entire genes into the genome that include the SNP under study, in effect creating a level genetic playing field on which to judge the contribution of each SNP to disease.

11:06 Weaver recommends those interested in more information on the field see the National Center for Biotechnology Information and the UCSC Genome Browser.

Immunogenome meets computing power

Welcome to the second podcast in the new series from the Mix on the emerging field of immunogenomics.

I recorded the interviews on the subject with national experts from UAB, Harvard, Stanford and the NIH at a recent symposium organized 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.

Immunogenomics is using new genomics tools to unravel the complexity of the human immune system and related diseases. Among the most important of genomics tools are microarrays, which enable researchers to measure the expression levels of many genes at once, and bioinformatic programs, which identify patterns in the massive data sets generated during genomic analysis.

Our guest for this podcast is meeting presenter Stephen Quake, D.Phil., professor in the Department of Bioengineering at Stanford and a Howard Hughes Medical Institute investigator. Quake specializes in microfluidic large-scale integration (LSI), in which he use his "lab on a chip" (a fluid-containing maze of channels, valves and wells on a microchip) to achieve high-speed, automated analysis of biological problems.

Our discussion covered how, by coming up with technologies that more precisely measure biological processes, the field has revealed new laws of nature at work in the body.


Show notes from the interview

:49 Immunogenomics, says Quake, can be defined as the sequencing and study of genes involved in the performance of the human immune system — genes whose expression pattern is in constant flux.

1:45 Right now you can't go to the doctor and ask him or her to give you a molecular diagnostic test measuring the health of your immune system, but such tests may be coming with the help of immunogenomics. In the future, such tests may be used in combination with therapies that adjust your immune response when it's too sensitive (autoimmune disease) or too weak (vulnerable to infectious disease).

2:52 Technology development is part and parcel with advances in immunogenomics. Quake's original training was in physics, with its 300-year tradition of precision measurement, which helped him to develop new measurement technologies for biological systems.

3:12 Biology was revolutionized time and time again in the 20th century by new technologies, from chromatography in the early part of the century to gene sequencing and genomic technologies in the latter half.

4:20 High-speed testing, or high-throughput technologies, have allowed for complex, massive experiments that could never have been conceived before their advent. The modern era is characterized by continual leaps in computing power, and that same type of technological scaling has now moved into the analysis of genomic information.

5:34 Computing power helps to resolve the complexity of the human immune system (now recognized as more complex than originally understood) and to pursue simple ideas.

5:59 The field of immunogenomics is young, perhaps starting with a zebrafish model paper out of Quake's lab in 2009. His early work in immunogenomics was focused on answering basic questions about the immune system, such as how many antibodies the human body contains.

7:13 The next big milestones in the field will include figuring out how to intrepret immunogenomic data in the context of a given event, like getting vaccinated or contracting an infectious disease. Lots of labs are working in this area, and it will be exciting as they reach their conclusions.

8:22 Immunogenomics is still focused on basic questions about how to measure the immune system with genomics tools. It will be some time before the field can launch an immune version of the Human Genome Project (the Human Immunogenome Project?).

9:03 With the field being so new, there our no textbooks on it nor are there yet review papers to recommend, although some are being written right now. For those with a deep interest, says Quake, the best course may be to search the literature by keyword using PubMed, and he invites all to look up his papers, which are listed by topic at his website.

About the podcaster:

Greg Williams @gregscience @themixuab is research editor at the University of Alabama at Birmingham. 

The first podcast in the immunogenomics series, which debuted on Oct. 5, 2012, featured S. Louis Bridges Jr., M.D., Ph.D., director of the Division of Clinical Immunology and Rheumatology within the UAB School of Medicine.

Tune in next Friday, when we will talk with symposium presenter Casey Weaver, M.D., professor in the Department of Pathology with the UAB School of Medicine.

New series on the human immunogenome

Most of the time The Mix covers general research topics, but for the next several Fridays we will feature a podcast series focused on the emerging field of immunogenomics. Guests will include nationally recognized experts in this area from UAB, HudsonAlpha, Harvard, Stanford and the National Institutes of Health.

We recorded the interviews live 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.

Immunogenomics as a field is using new genomics tools to unravel the complexity of the human immune system and related diseases, which are now known to include heart disease, neurological disease and cancer because of their interplay with inflammation. The work promises to improve diagnostic tools and offer new treatment approaches.

Among the most important of genomics tools are microarrays, which enable researchers to measure the expression levels of many genes at once, and bioinformatic programs, which identify patterns in the massive data sets generated during genomic analysis of individuals and populations.

Our first guest in the series is S. Louis Bridges, Jr., M.D., Ph.D., director of the Division of Clinical Immunology and Rheumatology within the UAB School of Medicine and deputy director of the UAB Comprehensive Arthritis, Musculoskeletal, and Autoimmunity Center. Tune in next Friday, when we will talk with Stephen Quake, D.Phil., professor in the Department of Bioengineering at Stanford.




Show notes for the interview:

1:09 Immunogenomics can be defined as the use of the tools of genomics to study human immune cells, and to define the mechanism by which immune-related diseases damage the body. 

2:02 Rheumatoid arthritis is the most common autoimmune disease, in which immune cells called antibodies come to target the body's own tissues.

2:47 In many ways, RA represents a cogent example of the intersection between immunology and genomics in that about 30 percent of the risk for the disease is based on your genes. In addition, small changes in more than 35 different genes contribute to that risk.

3:39 Bridges and colleagues founded the CLEAR registry, which stands for Consortium for the Longitudinal Evaluation of African Americans with Early Rheumatoid Arthritis. The registry compares the incidence and severity of RA in African-Americans against other ethnic and racial groups over time to better understand how immune-system mechanisms cause damage. Past studies have found that RA is more severe in African-Americans than in whites.

4:42 Researchers are working to understand the genetic basis of RA severity in African-Americans in part by examining single genes (RANK ligand, peptidase) known to be associated with disease severity or early onset. Bridges and colleagues have also been conducting genome-wide association studies, which look at every piece of code making up every gene (nucleotide) in a group of people to identify the differences seen only in people with a certain condition. In many cases, such studies reveal that networks of genes contribute to a disease, as opposed to a problem with the code of any single gene.

5:40 All races share 80 to 90 percent of the genetic background leading to RA, so perhaps 2 to 5 percent of genes vary by race, says Bridges.

6:02 In some whites, a gene called PTP-N22, for instance, has randomly undergone a small change in its code called an SNP (single nucleotide polymorphism). People who happen to have that change in PTP-N22 are 1.9 times as likely to develop RA.

7:09 A change in a single piece of code out of 3 billion base pairs making up the human genome, if it's in the wrong spot, can contribute to either the incidence or severity of RA. Such changes may predict which patients will go on to see their joints destroyed.

7:56  Immunogenomics work will have its first impact in the clinic in the form of a new wave of identified biomarkers that predict which patients will do well on which treatments. Further down the road, Bridges sees the field identifying more specific subsets of cells most responsible for RA-related damage, which could in turn lead to the development of more targeted treatments.

9:44 Bridges recommends that members of the general public interested in learning more on RA and related research visit the Mayo Clinic's RA pages. Researchers may want to look up the work of Robert Plenge, M.D., Ph.D., assistant professor of medicine at Harvard Medical School, whose interview is coming up as part of this podcast series in a few weeks.

About the podcaster:

Greg Williams @gregscience @themixuab is research editor within Media Relations at the University of Alabama at Birmingham.