The good doctor

“Haitian history is a chronicle of suffering so Job-like that it inevitably inspires arguments with God, and about God,” wrote George Packer in the January 25th issue of The New Yorker.

Packer then offered a litany of events and circumstances – from slavery, revolt and oppression, to American occupation and neglect, to extreme poverty, political violence, coups, gangs, and hurricanes, “and now an earthquake that exploits all the weaknesses created by this legacy to kill tens of thousands of people.”

Packer could have added that the small island nation had been plagued by endemic diseases including malaria, tuberculosis and, beginning around 1979, HIV/AIDS. Indeed, given a nearly nonexistent healthcare system at the time, Haiti had minimal defenses against the onset of that epidemic.

In 1983, while working for a medical television network aimed at physicians, I learned that the CDC had named Haitians along with three other groups – homosexuals, heroin addicts and  hemophiliacs – as high risk factors for what was then called HTLV infection – the “4H Club,” as some in the mainstream news media benightedly put it.  Ashamed to say that we who should have known better chuckled at this flippancy.

And so, during the period that the disease became increasingly identified with Haitian immigrants tothe U.S., this stigma borne of fear, confusion and racism singled out Haiti as the only country to suffer the consequences – this for a nation in which tourism was the economic backbone.

“It killed tourism in Haiti,” said Dr. Jean W. Pape in a 2006 interview. “Within a year the tourism industry decreased by 80 percent… Goods manufactured in Haiti could not be sold in the U.S.” 

And Haitians in the U.S. found it tougher finding work or selling their homes.

Dr. Jean Pape

Who is Jean Pape? He is a physician and scientist , and a bona fide hero. Honoring “heroes whose actions and courage make the world a better place,” the U.N. has praised Pape’s “achievements, courage and inspiration in contributing to breaking the silence on HIV/AIDS.”

Understanding that a solid research base was needed in Haiti in order to develop the most effective anti-AIDS strategies,  Pape established the Groupe Haitien d’Etudes du Sarcome de Kaposi et des Infections Opportunistes (GHESKIO), in 1982. The group integrates patient services, health research, and training in HIV/AIDS and inter-related diseases.

A professor of medicine at Cornell and a professor at the State University of Haiti, Pape also established Cornell’s Tropical Medicine and Infectious Disease Research Unit in Port-au-Prince. 

After completing his medical training at Cornell in 1975, he returned to his native Haiti to study childhood diarrhea.  He noted an increase in adult mortality related to diarrhea and with GHESKIO published the first comprehensive description of AIDS in the developing world in 1983. 

Since the January 12th earthquake,  GHESKIO and the good Dr. Pape has been providing humanitarian assistance and emergency care to literally thousands affected by the disaster and continues to provide life-saving medications to people with HIV/AIDS.

For a glimpse into the harrowing social and medical issues now facing Dr. Pape and GHESKIO, see this January 28, 2010, update he coauthored in The New England Journal of Medicine.

Visit GHESKIO  for a recent NBC Nightly News interview with Dr. Pape.

Les Lang

TB or not TB

 In the Shakespearean sense, this is a brief yet knotty tale of granulomas, of organized aggregates of immune cells in which things are not what they seem.

 Viewed through the fog of traditional belief, granulomas, the nodules that are a hallmark of tuberculosis, are heroes in stemming growth of the infecting mycobacteria.

 Now it appears that science’s sunlight has dissolved a century of fog.  Analysis of mycobacteria infections in tiny zebrafish embryos reveals that the early granuloma actually facilitates mycobacterial growth.  

Enough of this overwritten drivel!  ”The play’s the thing, ” the bard said. 

In brief, new research has discovered the signaling pathway by which a granuloma encourages TB pathogenesis.  And finding how to block that pathway may lead to new therapies for TB and other serious disorders. 

TB bacteria infect host macrophages in a larval zebra fish and prod epithelial cells to produce MMP9, a signaling protein associated with worsening infection. The MMP9 stained green in this mount, while the macrophages in the tubercle stained red. Credit: J.M. Davis and T. Pozos, University of Washington

In a report of the study in Science, on January 22, 2010, John F. Rawls, Ph.D., assistant professor in the UNC departments of cell and molecular physiology and microbiology and immunology,  joined co-authors from the University of Washingtion.

Their study identified a new molecular pathway that infecting mycobacteria use to coerce disease-fighting cells to switch allegiance and work on their behalf.  

Basically, the bacteria residing with immune cells called macrophages secrete the small protein ESAT-6, long implicated in virulence, which then induces nearby epithelial cells to produce the enzyme Matrix Metalloproteinase 9 (MMP9). 

Here the ball really gets rolling, as MMP9 secretion by epithelial cells is ramped up in the vicinity of an infected TB macrophage.  The enzyme’s action draws in uninfected macrophages to join the infected ones, thereby expanding the granuloma. 

Thus, according to the new research, TB bacteria simultaneously suppress the inflammatory action of macrophages to create a safe haven in them, while nudging epithelial cells to signal for the arrival of more macrophages which, in turn, are inducted into granuloma expansion. 

“The implications of these results extend beyond TB to other types of inflammation,” says Rawls. “This novel signaling cascade from bacterium to epithelium to macrophage could represent a common strategy by which other microorganisms or other factors influence the process of inflammation.” 

And so it is hoped that this discovery could help raise the curtain on some exciting innovative therapies that will bring it down on TB, arthritis, and other inflammatory disorders. Fini.

Les Lang

Of blank slates and embryo development

The DNA contained within each of our cells is exactly the same, yet different types of cells – skin cells, heart cells, brain cells – perform very different functions.

The ultimate fate of these cells is encoded not just in the DNA, but in a specific pattern of chemical modifications that overlay the DNA structure. These modifications, or epigenetic markers as they are called, are stably carried in our genomes — except for at times when the cells change their fate, such as what occurs when the sperm meets the egg. Then they are erased completely. 

A fertilized egg prior to division. Two nuclei (one from the egg and one from the sperm) are visible in the center. Photo courtesy: Stan Beyler, PhD, UNC A.R.T. lab)

Researchers at the UNC School of Medicine have discovered a protein complex that appears to play a significant role in erasing these epigenetic instructions on sperm DNA, essentially creating a blank slate for the different cell types of a new embryo to develop. The protein complex – called elongator – could prove valuable for changing cell fate, such as converting cancer cells to normal cells, as it may be able to reactivate tumor suppressor genes by removing the epigenetic modifications that often prevent them from curbing the proliferation of cancer cells. 

The discovery may also have implications for stem cell research by providing a tool to quickly reprogram adult cells to possess the same attributes as embryonic stem cells, but without the ethical or safety issues of cells currently used for such studies. The results of the study appear on-line in the Jan. 6, 2010issue of the journal Nature. 

“The implications of such research have always been clear, and that is why for years researchers have tried to identify a factor responsible for erasing these epigenetic markers,” said senior author Yi Zhang, Ph.D., Howard Hughes Medical Institute Investigator and Kenan Distinguished Professor of Biochemistry and Biophysics at UNC. He is also a member of the UNC Lineberger Comprehensive Cancer Center. 

Epigenetic markers are essentially chemical tags attached to the genomes of each cell, determining which genes will be turned on or off and, ultimately, what role that cell type will have in the body. One way this comes about is through DNA methylation, a process by which methyl groups are stamped onto cytosines — one of the four bases of DNA — to produce a characteristic pattern for a particular cell. 

During fertilization, the paternal genome derived from the sperm is actively demethylated, removing these methyl tags quickly before cell division, while the maternal genome is demethylated passively. The new methylation pattern will be reestablished at a later stage. 

“Several previous studies have identified factors that can perform gene-specific DNA demethylation, but ours is the first to link a protein complex to global DNA demethylation that correlates to germ cell to somatic cell transition,” Zhang said. 

For further details, click here.

Les Lang

Fish gotta swim, bacteria gotta…walk

The ability to swim comes as naturally to bacteria as it does to fish. In the wet, microbes propel themselves through fluids using a whip-like extension called a flaggella.

But when on solid surfaces, the little beasties also can walk, twitching along using little fibrous legs called pili.  And when they adhere to host tissue, including that of  homo saps like you and me, the pathogenesis of bacterial infection, its establishment and spread elsewhere in the body, largely depends on bacterial ability to walk. 

Now what if it were possible to prevent infection by stopping bacteria in their tracks? New research at the  University of North Carolina at Chapel Hill appears to have taken a major step in that direction.

The UNC researchers have discovered that a single atom can control how bacteria walk.  By resolving the structure of a protein involved in the motility of the opportunitistic human pathogen Pseudomonas aeruginosa, the scientists identified a spot on the bacteria, that when blocked, can indeed stop  bacterial motility cold.  

“When it comes down to it, a single atom makes all the difference,” said senior study author Matthew R. Redinbo, Ph.D., Professor of Chemistry, Biochemistry and Biophysics at UNC. His findings appear in the Dec. 28, 2009, early online edition of the Proceedings of the National Academy of Sciences.

The binding and release of a single atom (shown in light blue) to a bacterial protein is necessary for microbial walking and infection.

For the last few years, Redinbo and his team has been working in close collaboration with Matthew C. Wolfgang, Ph.D., an Assistant Professor of Microbiology and Immunology and a member of the Cystic Fibrosis/Pulmonary Research and Treatment Center at UNC, trying to figure out how bacteria’s tiny legs or pili function.

The researchers began to look at one of the many types of pili, called type IV pili. Type IV pili are basically long, dense fibers that bacteria assemble (extension) or disassemble (retraction) quite quickly.

“These pili act as grappling hooks – the bacteria extend the fibers out, the fibers attach or stick to a surface, and then retracted back into the bacteria, pulling it along,” said Wolfgang. “This crawling movement is called twitching motility, and without it Pseudomonas, a common cause of hospital-acquired pneumonia would never be able to move from the lung tissue into the bloodstream, where the infection becomes lethal.”

The researchers knew that inside the cell lie the tiny little motors – called ATPases – that drive the extension and retraction of the pili. One of these ATPases is the extension motor, which sticks the bacteria’s leg out. The other ATPase is the retraction motor, which pulls it back in. But what wasn’t clear was how the two motors were coordinated so that pushing and pulling didn’t occur at the same time. That is what Redinbo and Wolfgang set out to discover.

First, they resolved the crystal structure of the Pseudomonas PilY1 protein, which other research had shown was necessary for the creation of pili. They made large amounts of the protein, coaxed it out of solution so that it formed a crystal, and then put the crystal under intense x-ray beams through a process called x-ray diffraction that resulted in a series of spots.

Based on the spots, the researchers calculated what the protein looked like. When they studied the structure, one particular site – the binding site of a calcium atom – looked like it could be important for the function of the protein. So the researchers began to tinker with the site, looking to see if the changes they made affected the protein’s behavior.

When they changed the protein so it could no longer bind calcium, the bacteria couldn’t make any legs. When they fooled the protein into thinking it was forever bound to calcium, the bacteria made legs but couldn’t retract them, essentially becoming paralyzed. The results suggested that the protein has to bind calcium to make legs, but it also has to be able to let go of the calcium to pull the legs back in.

“We found it pretty remarkable that the binding of a single atom to a protein that is outside the cell is sufficient to tell these motors that are inside the cell to either stop pushing or stop pulling,” said Redinbo.

He says they are currently using a combination of genetics and biochemistry to figure out how this long-distance communication is possible.

 

GINA swings into action

As of Saturday November 21, 2009, GINA entered the building.

Eighteen months after President Bush signed it into law, the Genetic Information Nondiscrimination Act of 2008  is officially effective.

GINA prohibits employer discrimination based on genetic information and also prohibits health insurers from denying coverage or setting rates based on a person’s genetic makeup, such as a predisposition to a disease.

This legislation is especially welcome and timely given the fact that we’re entering a new medical era in which our genomes will be increasingly explored to aid in diagnosis and treatment of disease, says James P. Evans M.D., Ph.D, Editor-in-Chief of the journal Genetics in Medicine and the Bryson Professor of Genetics and Medicine at UNC.

Dr. James P. Evans

“It is difficult enough to have to contend with a genetic disorder or disease predisposition without the added agony of worrying about what that knowledge might do to your ability to get insurance.”

Still, while a step in the right direction, GINA doesn’t afford any protection to individuals with regard to life insurance, disability or long term care insurance.

And unless comprehensive health reform  establishes requirements for insurers to offer coverage to all Americans who apply and prohibits them from denying coverage or charging more based on overall health, GINA does nothing to protect individuals from insurance discrimination once they have developed signs or symptoms of a genetic (or any other) disease.

Meanwhile,  GINA’s impact on genetic research subject recruitment remains unknown.  The government’s Office of Human Research Protections  offers an informational guidance on GINA implications for investigators and institutional review boards involved in HHS-funded genetic research.

But it remains to be seen whether or not people would be more likely now to participate in genetic research studies, to volunteer for genetic testing.

Les Lang

Humanized mice and HIV prevention

An estimated 33 million people are now infected with HIV worldwide. But a not so small reason why AIDS has slipped from the top of the news is the general agreement among experts that an effective HIV vaccine could be many more years in the making.

The situation has led some researchers to study alternative preventive strategies, including pre-exposure prophylaxis with antiretroviral drugs.

One scientist whose work in this area is of special importance is  J. Victor Garcia-Martinez, Ph.D., professor of medicine, division of infectious diseases at UNC, and a member of the university’s Institute for Global Health and Infectious Diseases.

A newcomer this year to the Carolina campus, Garcia-Martinez  carries  a broad pallette of research areas: humanized mice, retrovirology, AIDS, stem cell biology, and human gene therapy.

J. Victor Garcia-Martinez, Ph.D.

Humanized mice? Yes, since their inception less than 20 years ago, mice carrying transplanted, functional human tissue, genes, cells or organs have been used experimentally as in vivo human  stand-ins in biomedical research.

Today, we have a number of humanized mouse models with reconstituted immune systems.  And it may well be that the best of the bunch for HIV/AIDS research is the so-called humanized bone marrow-liver-thymus (BLT) mouse   developed by Garcia-Martinez .

With immune systems reconstituted from human bone marrow, liver and thymus transplants, BLT are the model mice that come with all the goods necessary in one package to simulate immune system functions of  Homo sap.

Here are a few reasons why: BLT mice could provide a model for prevention of intravaginal HIV infection. In one study, they have been shown to be susceptible to HIV transmission via a single intravaginal exposure.

Intravaginal exposure of these mice to HIV led to systemic HIV infection coupled with a rapid loss of human CD4⁺ T cells from the gastrointestinal mucosa, a known  hallmark of acute HIV infection in humans.

In this same  study, vaginal HIV infection was prevented in the BLT mice by pre-exposure prophylaxis using a combination of antiretroviral agents.

And in another study led by Garcia-Martinez, BLT mice were shown to be susceptible to HIV infection after a single intrarectal inoculation. This, too, coupled with loss of  CD4⁺ T cells from gut-associated lymphoid tissue and other evidence “closely mimics those observed in HIV infected humans.”

You might say these studies go beyond proof-of-concept to powerfully demonstrate why Garcia-Martinez’s mouse model holds promise for the preclinical evaluation of microbicides and antiretroviral prophylaxis regimens against HIV.

Click here for more details on the man and his work. And check this blog for reports of new research.

Les Lang

Predicting drugs’ side effects, new uses

Bryan Roth, MD, PhD

It should come as no surprise that lots of target-specific drugs are no so targeted. After all, many of the most successful drugs on the market today are being prescribed for uses that are quite different from the ones they were originally designed to treat.

Sometimes serendipity in the form of unforeseen side effects happens. That’s how today’s Viagra avoided the pharmaceutical dustbin.  Having flunked a Phase 1 clinical trial as a heart drug for angina, researchers noted it was associated with penile erections. The rest is history, or herstory… whatever. 

Now, scientists at the UNC School of Medicine and the University of  California, San Francisco, have developed and tested a computational technique to predict a new drug’s side effects and new target diseases for existing drugs.

Their article published online November 1st in Nature, describes a “chemical similarity” approach using “statistics-based chemoinformatics” that compares drug targets by the similarity of their mutual binding partners, or ligands.

Co-senior study author Bryan Roth, M.D., Ph.D., professor of pharmacology and director of the National Institute of Mental Health Psychoactive Drug Screening Program at UNC, says  “We may now have a way to predict what side effects are likely to occur from treatment before we even put a drug into clinical testing.” 

Read our news release here.

Les Lang

FLASH dances with death and mRNA

Whether it was Daniel DeFoe or Benjamin Franklin, whoever coined the phrase, “Nothing is certain but death and taxes,” clearly hadn’t a clue of another of life’s immutable pairings:  histone proteins and DNA.

Histones are the chief protein components of chromatin — the protein/DNA combo of which chromosomes are made — and they act as a scaffold to allow the packaging of DNA into a condensed form that fits inside the nucleus of a cell. As the DNA interacts with histones and with metabolic signals from within the cell, these proteins help regulate gene expression.

But how does the histone component of this dynamic duo get started in the first place?  The answer, according to new research from UNC,  appears in [a] FLASH.

This protein is already shown to play a role in initiating apoptosis, or the normal process of programmed cell death, and is now the latest key player in the molecular dance essential for DNA replication within cells.

According to senior study author Zbigniew Dominski, Ph.D., associate professor of biochemistry and biophysics, the new study demonstrates that FLASH is  required for the proper synthesis of histone messenger RNA, which gives rise to histone proteins.

“FLASH is crucial for the production of histone messenger RNA, without which the cell can’t make the histone proteins around which DNA is packaged,” says Dominski. “Our study suggests for the first time that a potential link exists between the processes of histone messenger RNA formation and apoptosis.”

The research is described in the October 23^rd issue of the journal Molecular Cell.

For the study, Dominski adapted a laboratory system that reproduces in the test tube what normally occurs in the cell when FLASH participates in the biochemical cleavage event that results in mature histone messenger RNA. This enabled his team to explore what might occur when FLASH was added or removed.

“We could then figure out exactly what portion of FLASH would restore the protein’s function in generating histone mRNAs and remarkably, only the first 100 or so amino acids are required.  The remaining 2,000 amino acids of this large protein likely control other processes in the cell, including apoptosis and DNA replication” he explained.

Co-author William F. Marzluff, Ph.D., is Distinguished Professor of biochemistry & biophysics. He notes that FLASH is the first component found in this protein complex that integrates or initiates many cellular functions — DNA replication, apoptosis, histone production.  “Having this small piece of the puzzle makes it a lot easier to identify others.”

Except for a certain somebody who originally paired the certainty of death and taxes.

Les Lang

From gene deletion to schizophrenia?

Scientists have long thought the faulty neural wiring that predisposes individuals to behavioral disorders like autism and psychiatric diseases like schizophrenia must occur during development. But no one has ever shown that a risk gene for the disease actually disrupts brain development.

Now, UNC scientists  have found that the 22q11 gene deletion on chromosome 22 – a mutation that confers the highest known genetic risk for schizophrenia – is associated with changes in the development of the brain that ultimately affect how its circuit elements are assembled.

In a genetic animal model, the researchers discovered that the gene deletion alters the number of a critical subset of neurons that end up in the brain’s cerebral cortex – the region critical to reasoning and memory. The defect also causes another type of nerve cell – called GABAergic neurons – to be misplaced within the brain’s cortical layers, resulting in a subtle miswiring of the organ.

“For practically ever other disease, we know what cells take a hit,” said senior study author Anthony LaMantia, Ph.D., professor of cell and molecular physiology and co-director of the Silvio M. Conte Center for Research in Mental Disorders at the UNC School of Medicine.

“For multiple sclerosis the myelinating oligodendrocytes in the brain falter, for Lou Gehrig’s disease the motor neurons in the brain stem degenerate. But we really had no idea what was happening in schizophrenia, or in any of the psychiatric diseases for that matter – until now.”

The study was presented October 17, 2009  at the Society for Neuroscience meeting in Chicago, by Daniel Meechan, Ph.D., post-doctoral fellow in the LaMantia laboratory and the first author of the recent paper in Proceedings of the National Academy of Sciences that details the findings.

Les Lang

GO accelerator for genome research

Ever since the first genome sequence was published in 2001, scientists have been working to figure out what the sequence means.  An analogy is walking across a desert and finding a large book in a language you don’t know, then trying to figure out what the book is saying.

“In the case of the human genome, the book is a blueprint to building cells—and ultimately—the whole human.  But we don’t yet understand its language,” said Morgan Giddings, Ph.D., associate professor of microbiology and immunology and of biomedical engineering at the University of North Carolina at Chapel Hill.

Morgan Giddings, Ph.D., left, and Xian Chen, Ph.D., right. Photo by Courtney Potter

Giddings and UNC colleague Xian Chen, Ph.D., associate professor of biochemistry and biophysics, have been developing methods for decoding the human blueprint by studying the things the blueprint produces: proteins.  They relate the proteins back to the blueprint itself, to further decode the language of the genome blueprint.

Giddings and Chen have been awarded a $1.6 million 2-year “Grand Opportunities” (GO) grant from the National Human Genome Research Institute to accelerate this research.  Their effort will be part of a consortium of investigators studying the human genome blueprint, titled the “ENCyclopedia Of DNA Elements” (ENCODE).  The consortium’s overall goal is to assemble a comprehensive catalog of functional elements in the human genome.

With their GO grant, Giddings and Chen will generate, analyze, and release to the public large-scale data sets that allow linking of the protein products in cells to their genomic blueprints.  According to Giddings, “this will significantly promote our understanding of the language of the human genome, enhancing efforts to solve pressing human health issues like heart disease and cancer by understanding how errors in the blueprint lead to disease, and how we might fix those errors.”

Giddings is a member of the Carolina Center for Genome Sciences, and Chen is technology development director for the UNC Proteomics Core.

As to impact  on the local North Carolina economy, the new grant is expected to  bring 4-6 new high-tech jobs to the Triangle.

NHGRI has awarded approximately $22 million of American Recovery and Reinvestment Act 2009 funds to support research aimed at identifying and understanding the genome’s functional elements.

Les Lang