From Rutgers: “Probing How a Gene and Some Proteins Might Point a Brain toward Autism”

Rutgers University

May 24, 2016
Robert Forman

Rutgers University-Newark scientists seek to chart a chain reaction that starts with a mutation. Nora Luongo

The development of the human brain, which begins in the womb and continues long after birth, is an elaborate construction job. Guided by a person’s genes, and the proteins whose production they spawn, tens of billions of neurons (nerve cells) somehow find a way to come together one by one until the structure of the brain is complete. Yet the blueprints are not always followed and scientists are convinced that this produces variations in human behavior, one of which is autism.

“The brain, how it works, is based on one neuron connecting to another and then another, and forming these circuits,” explains Tracy Tran, an assistant professor in the Department of Biological Sciences at Rutgers University-Newark (RU-N). “That’s how the gross function of complex behavior develops.” The circuits form, she says, when each neuron extends a process, called an axon, secreting neurochemicals (neurotransmitters) used to communicate, via electrical impulses (synapses) with another neuron, usually on the dendrites. In the most simplistic example, the axon of neuron A would communicate with the dendrites on neuron B, and the axon from neuron B will pass along the processed information to the dendrites of neuron C, and so on until the loop of information comes back to first neuron – a simple circuit.

Tran leads a team that is looking into what makes the circuits form as they do, and potential ways to – in effect – rewire those connections to make them more conducive to healthy brain function during disease. The fundamental concept is that if we know how something is put together, then hopefully, we would be more equipped to fixing it when its broken or in the case for the brain when it is not functioning properly. As Tran describes it, what the team wants to know is, “how does any one particular neuron know to connect with neuron B and not neuron C or D or E? It must precisely connect with its proper target,” she explains, “because if it doesn’t that’s what results in many of the neurological diseases that we see such as autism.”

Scientific evidence suggests that a large family of proteins called semaphorins influences which neurons connect with each other during neural development. The proteins also appear to regulate the growth and physical structures of dendritic spines, which protrude, as tiny extensions, from the dendrites like thorns on a rosebush. Dendritic spines are sites for stimulatory (or excitatory) synapses, therefore, the more spines a neuron has – increasing the stimulation it can receive from other nerve cells, the more overloaded a neuron might become. It is a bit like having 20 spotlights shining into a person’s eyes where having just two lights would be much better. “If you don’t have the light you don’t see at all,” Tran explains, “but if you have too much of it, that’s not good.” Tran believes autism symptoms can arise when certain neurons are imbalanced with the number of stimulations they receive.

Along with RU-N colleagues James M. Tepper, a distinguished professor in the Center for Molecular and Behavioral Neuroscience; and Michael Shiflett, a research assistant professor of psychology with expertise in animal behavior, Tran wants to learn from start to finish how semaphorins affect these brain development processes. It is knowledge they then hope to apply to human autism.

Tran assembled this team with one of six Initiative for Multidisciplinary Research Team (IMRT) awards that RU-N granted to members of its faculty in 2015. The awards are funding varied research projects in both the physical and social sciences.

With her team’s $80,000 award, Tran will breed laboratory mice with a gene mutation that stops the production of semaphorins, causing the mutant mice to produce extra-spiny dendrites in their brains as is observed in humans with autism. Then – using equipment in his lab that measures brain activity in exquisite detail – Tepper will examine both the brains of those mice and brains of genetically normal mice, neuron by neuron, and record how differently nerve signals move through them. Shiflett will then compare the behaviors of the two sets of mice, with tests designed to detect any autistic tendencies.

Of course, many aspects of human autism are too sophisticated to appear in a creature such as a mouse. At the same time, says Shiflett, “you also can measure all sorts of behaviors in mice, from very simple behaviors like locomotion and processing of touch and sound, to fairly complex kinds of behaviors like decision-making and complex-attention kinds of tests. A lot of these tests are based on understanding the human condition.”

Shiflett will document how energetically mice with the gene mutations examine colorful new objects added to their environments, compared with how they treat similarly attractive objects they have seen before – a potential proxy for ways that humans with autism react to various people. Similarly, Shiflett will evaluate repetitive motions of the experimental mice, which also have an analog in people with autism.

The work by the RU-N team is extremely preliminary, and the gene connected with semaphorin is just one of hundreds that science has linked with autism. Tran knows she is addressing just a small slice of the spectrum. Still, it is conceivable that one day, gene therapy could help regulate brain formation before birth. Or, researchers might build on data from Tran’s lab suggesting that, at least in a culture dish, when semaphorin is added to neurons, “within hours we see a dramatic decrease in the number of spines.” Says Tran, “this gives a clue that these molecules can actively restrain the number of spines being formed in a very short time.” If hopes are realized, the finding could translate one day into effective treatments of the living human brain.

Shiflett says the IMRT award has been essential to moving the work forward, because none of the scientists on the team could have executed such a project in isolation. “There are so many benefits to collaborating,” he notes. “You can do so many more things.”

“We hope that we will find some really interesting results, and continue on,” adds Tran. “That’s the thing about science. After you find the answer to one question, that opens the door for many, many other questions. That’s part of the excitement.”

See the full article here .

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Rutgers, The State University of New Jersey, is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

From Rutgers Today: “Pursuing the Destruction of HIV-infected Cells”

Rutgers University

5.18.16
Dory Devlin

An oral drug used to treat an illness unrelated to HIV eradicated infectious HIV-producing cells in lab cultures while sparing uninfected cells – and suppressed the virus in patients during treatment and for at least eight weeks after the drug was stopped, according to results of a clinical pilot trial and researchers at Rutgers University and Dartmouth College.

The findings*, published May 18 in the scientific journal PLOS ONE, point to development of a promising HIV treatment that could destroy the HIV DNA harbored in HIV-infected cells. Current HIV-AIDS treatments center on antiretroviral drugs that, when taken in combination for all of a patient’s life, can prevent the growth of the virus but not kill or cure it.

“For the first time, we show that it’s possible with a systemic drug to selectively kill the AIDS-causing HIV-infected cells,” said Hartmut Hanauske-Abel, a researcher from Rutgers New Jersey Medical School, a lead author of the study with appointments in the departments of Obstetrics, Gynecology and Women’s Health; Pediatrics; and Microbiology, Biochemistry and Molecular Genetics.

Treatment that targets the DNA in HIV-infected cells has been challenging because the persistent, incurable human immunodeficiency virus is able to insert its own DNA into the DNA of any infected cell while disabling that cell’s ability to die to save other cells from a viral invasion. The researchers found that the oral drug, deferiprone, like the topical anti-fungal medicine ciclopirox that they previously studied, reactivates the “altruistic suicide response” of an HIV-infected cell, killing the HIV DNA it carries.

The clinical pilot trial – conducted by the Toronto-based firm, ApoPharma Inc., which markets deferiprone – involved 26 consenting volunteers, both HIV-infected and healthy. Some participants received placebos, others the drug at two different doses. Analyzing the raw data, the researchers found that of seven participants with HIV whose serum registered a necessary threshold concentration of the drug while taking it during the seven-day protocol, six showed positive HIV responses while in treatment. Participants who completed the entire protocol maintained their responses after drug treatment was stopped for eight weeks.

The authors cautioned that the findings do not prove that deferiprone in its current form is a safe and effective treatment for HIV. But the findings do provide researchers with ample evidence to pursue funding for larger clinical trials and to use the drug as a lead for future drug development, they said. The main function of this proof-of-concept trial was to learn that it is possible to have a drug that knocks down HIV and prevents its rebound.

“The discovery raises the hope that HIV may not be able to develop resistance against this novel class of drugs,” said study co-author Paul Palumbo of Dartmouth’s Geisel School of Medicine. “It gives credence to the concept that like cancer cells, HIV-infected cells can be targeted and eliminated by a drug.”

Resistance commonly develops when treating HIV with widely used antiretrovirals. Despite the short, seven-day trial, deferiprone’s effect on reducing HIV blood levels was similar to a multi-week treatment with AZT, zidovudine, an antiretroviral commonly used to treat HIV. The anti-HIV effect of deferiprone persisted after the drug was stopped – “an effect quite different from all current antiretrovirals,” the researchers said.

Regulatory guidelines for developing new antiviral drugs for HIV focus on inhibiting viral production and avoid using agents that kill cells that are actively or latently HIV-infected. That’s why this group of researchers is focused on developing protocols for already approved drugs used for other medical treatments that show promise in eradicating HIV-infected cells, and on testing new combinations of those drugs for novel treatment protocols. Deferiprone, available for the past 20 years, is used in more than 60 countries to prevent death from blood transfusion-related complications during treatment of thalassemia, an inherited blood disorder in which the body makes an abnormal form of hemoglobin.

The HIV-AIDS pandemic persists. Worldwide, 36.9 million people live with HIV-1, yet only 14.9 million (40 percent) are treated. The study also notes increases in HIV-1 infections in several U.S. cities in the U.S. and worldwide. At the end of 2012, an estimated 1.2 million people aged 13 and older were living with HIV infection in the United States, including 156,300 (12.8 percent) whose infections were not diagnosed, according to the Centers for Disease Control.

The study published in PLOS ONE is the result of a 15-year research effort by the joint senior authors, Dartmouth’s Palumbo of Dartmouth and Rutgers’ Hanauske-Abel . They integrated university-, government-, and industry-based researchers from the United States and Canada in a combined effort to define the testable prospects of this novel treatment strategy for HIV-AIDS.

*Science paper:
Drug-Based Lead Discovery: The Novel Ablative Antiretroviral Profile of Deferiprone in HIV-1-Infected Cells and in HIV-Infected Treatment-Naive Subjects of a Double-Blind, Placebo-Controlled, Randomized Exploratory Trial

See the full article here.

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Rutgers, The State University of New Jersey, is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

From Rockefeller: “New method gives scientists a better look at how HIV infects and takes over its host cells”

Rockefeller University

May 23, 2016
No writer credit found

Cell to cell: When HIV infects a cell, it programs the cell to express the viral protein Env, which the virus uses to spread to neighboring cells. Above, Env (red) produced by one infected cell has recruited other, uninfected cells, causing them to fuse, and their nuclei (blue) to cluster.

Viruses attack cells and commandeer their machinery in a complex and carefully orchestrated invasion. Scientists have longed probed this process for insights into biology and disease, but essential details still remain out of reach.

A new approach, developed by a team of researchers led by the Rockefeller University and the Aaron Diamond AIDS Research Center (ADARC), offers an unprecedented view of how a virus infects and appropriates a host cell, step by step. In research published* May 23 in Nature Microbiology, they applied their method to HIV, a virus whose genome is less than 100,000 the size of ours.

“HIV is truly an expert at living large on a small budget,” says first author Yang Luo, a postdoc at ADARC and a former graduate student at Rockefeller University. “We asked the question, how does such a compact virus manipulate the host cell to gain entry and replicate itself, all while escaping the immune system?”

Mapping HIV’s ‘interactome’

The study focused on two viral proteins known to bring about HIV’s infection of human white blood cells. The first one, called envelope or Env, sits on the surface of the virus and, by binding to receptors on the host cell, helps the membrane that encapsulates the virus fuse with the cell’s outer membrane. A second protein, Vif, destroys an enzyme that host cells produce to defend themselves against the virus.

In an effort to better understand how these two proteins function, the team wanted to map their interactome—meaning all the proteins with which they associate within a host cell. To accomplish this, the researchers needed to devise a way to isolate clusters of interacting proteins from cells during different stages of infection. Such experiments can be done by introducing a genetic sequence into the viral genome—a “tag” that acts like a piece of molecular Velcro, allowing one viral protein to be yanked out along with all the other proteins associated with it.

It sounds simple, but making it work took a decade.

“Inserting a tag sequence into small viruses is a challenge to begin with,” says corresponding author Mark Muesing, a principal investigator at ADARC. “If you disrupt their nucleic acid and protein sequences, you can easily compromise the virus’s ability to replicate. And HIV represents a particular challenge because it can quickly revert back to its original sequence.”

“We developed a technique to find places in the HIV genome where we can insert stable tags without affecting the virus’s capacity to proliferate. In effect, this allowed us to expand cultures of the infected cells along with the tagged viral protein,” he added.

The host’s contribution

Next, the researchers infected human cells with viruses carrying the tagged protein sequences, and were able to pull out and identify a large number of host proteins directly during the infectious process. This provided the first evidence that many previously underappreciated host proteins interact with the viral machinery during replication.

“Imagine you have a factory assembly line where only one component of, say, the stamping machine, actually touches the product,” says co-author Michael Rout, professor and head of Rockefeller’s Laboratory of Cellular and Structural Biology. “Other parts support and power the stamp. Likewise, within an infected cell, we can identify the components of a particular cellular machine, not just the piece that comes in contact with the viral protein.”

“Every host protein we pull out generates new questions,” adds co-first author Erica Jacobs, a research associate in Brian Chait’s lab. “Does it help the virus invade and coopt the host to replicate itself? Or does it harm it? The answers will not only help us understand the virus, but also shed light on our cells’ ability to defend themselves.”

One important discovery has already emerged from the lists of proteins. Viruses, including HIV, often attack as so-called virions, which are individual packets of protein and genetic code. But they can also pass directly from an infected to an uninfected cell, a more effective mode of transmission. To do so, the virus appears to use host proteins to construct a platform, a close junctional surface, between cells.

From the list of proteins that interact with Env, the researchers have identified cellular proteins predicted to contribute to this platform between cells. Because this route of transmission protects the virus in a sequestered environment, away from host defenses, the new findings may aid in the development of future anti-HIV therapies.

A live infection, step by step

According to co-author Brian Chait, Camille and Henry Dreyfus Professor and head of the Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, the new approach offers a rare glimpse into the process by which HIV invades and resurrects itself within a cell.

“Often, studies of this sort are done with viral proteins in the absence of a true viral infection “However, because viral infections are exquisitely orchestrated events, you are likely to miss all kinds of important details if you study the action of these proteins out of their proper context.”

“Deciphering the intricacies of virus-host protein interactions in space and time during the progression of an infection is remarkably powerful” says co-author Ileana Cristea, an associate professor of molecular biology at Princeton University. “The challenge is to discover which precise interactions are the critical ones.”

Todd Greco, a co-first author, and an associate research scholar and lecturer in molecular biology in Cristea’s lab, says that “even for host proteins within the same family, their relative stability within HIV-1 protein complexes can be very different. More broadly, by understanding these mechanisms we will better understand the coordinated responses of cells.”

*Science paper:
HIV–host interactome revealed directly from infected cells

See the full article here .

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The Rockefeller University is a world-renowned center for research and graduate education in the biomedical sciences, chemistry, bioinformatics and physics. The university’s 76 laboratories conduct both clinical and basic research and study a diverse range of biological and biomedical problems with the mission of improving the understanding of life for the benefit of humanity.

Founded in 1901 by John D. Rockefeller, the Rockefeller Institute for Medical Research was the country’s first institution devoted exclusively to biomedical research. The Rockefeller University Hospital was founded in 1910 as the first hospital devoted exclusively to clinical research. In the 1950s, the institute expanded its mission to include graduate education and began training new generations of scientists to become research leaders around the world. In 1965, it was renamed The Rockefeller University.

From Vandy: “Study explores gene’s role in protecting HIV patients from TB”

Vanderbilt University

Mar. 17, 2016
Bill Snyder
william.snyder@Vanderbilt.Edu

An international research team led by scientists from Vanderbilt University Medical Center has identified a genetic variant that protects people with HIV from developing active tuberculosis. The variant is near the gene encoding the infection-fighting cytokine IL-12.

The discovery, reported this month in the American Journal of Human Genetics,could lead to new treatments for TB, which is the No. 1 killer of patients with HIV in sub-Saharan Africa and which causes more than a million deaths worldwide each year.

HIV trimer

“It was a very exciting finding for us, particularly in light of the potential translational implications,” said the paper’s first author, Rafal Sobota, an M.D./Ph.D. student in the Vanderbilt Medical Scientist Training Program. Sobota earned his Ph.D. in Human Genetics last year and will receive his M.D. in 2017.

People infected with HIV, which suppresses the body’s immune system, are at higher risk of developing active TB once they are infected by the TB bacterium. Some HIV-positive people, however, do not develop active TB, even in areas such as sub-Saharan Africa, where the potentially fatal lung infection is rampant.

To find out why, Sobota and colleagues from Dartmouth College in Hanover, New Hampshire, and Case Western Reserve University in Cleveland, conducted a genome-wide association study of 581 HIV-positive patients in Tanzania and Uganda.

Although all participants were exposed to the TB bacterium, only 267 developed active disease over the span of at least eight years. The 314 patients who did not develop clinical TB represented an extreme resistance phenotype, which the authors believe increased the power to detect the association.

The identified variant was in a regulatory element of the gene encoding IL-12, IL12B. Subjects with one form of the variant were protected from active TB, while those with the other form were more likely to develop active disease.

The researchers also found that the protective variant is strongly selected for, being found in up to 45 percent of various populations in sub-Saharan Africa, while being absent in other parts of the world.

Previous studies have shown that patients with very rare inherited IL-12 deficiency are prone to developing severe cases of active TB. And in several studies of mice infected with the TB bacterium, induction of IL12B expression or direct inoculation with the cytokine protected the animals from developing active disease.

Sobota began the study as his dissertation topic over five years ago under the direction of his thesis advisor, Scott Williams, Ph.D., the paper’s senior author. Williams is now on the faculty at Case Western Reserve University.

“I was fortunate enough to travel to Tanzania for six months and recruit the patients for the study,” Sobota said.

A collaborator on the faculty at Case Western Reserve University, Catherine Stein, Ph.D., recruited the study participants in Uganda. Other co-authors included Nuri Kodaman, who also earned his Ph.D. in Human Genetics at Vanderbilt last year.

See the full article here .

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From FAAH at WCG: “FightAIDS@Home Researchers Test New Simulation Methods”

15 Feb 2016
By: The FightAIDS@Home research team

Summary
The research team for Phase 2 of FightAIDS@Home is developing and testing new ways to use the vast computing power of World Community Grid. Their goal is to build on the results from Phase 1 while using volunteers’ resources as efficiently as possible.

This molecule, known as AVX101124, was identified in Phase 1 of FightAIDS@Home as being important to our ongoing research.

Overview

Our FightAIDS@Home – Phase 2 team is getting acclimated to running the research software on this very powerful yet unconventional computational resource. We are analyzing preliminary results from the first batches of research tasks, which were used to test different simulation approaches, and honing in on the most efficient ways to use the vast amount of donated computing time. We have also been preparing a large set of new work units while retooling our data processing and analysis pipelines to keep up with the massive inflow of results.

Using BEDAM simulations for FightAIDS@Home – Phase 2 presents an enormous opportunity to refine and enrich the results from Phase I. However, before refining both hits identified in Phase 1 and new compounds studied by our HIVE Center collaborators, we need to develop and test new ways to run our software under the constraints imposed by the grid computing infrastructure.

Details

The current set of research tasks (‘work units’) was designed to serve three purposes. First, we evaluate how our new simulation schema tailored for free energy calculations using the distributed and heterogeneous resources of World Community Grid compares with the results of more traditional homogeneous high performance clusters. We have launched two different sets of simulations on World Community Grid that differ in how energy function parameters vary across many copies of each target ligand-protein complex being simulated. Second, the simulations allow us to revisit the calculation of binding free energies (binding scores) and prediction of binding modes (poses) for a well-studied dataset of HIV Integrase protein that we studied previously in the SAMPL4 binding free energy prediction challenge. By performing these different simulations on this benchmark set of complexes, we can design and optimize future batches of simulations to be as efficient as possible in terms of volunteers’ resources.

The first set of simulation results (experiments 0-52) are almost complete and have been analyzed. We anticipate that this first simulation scheme is vastly superior to the second scheme being tested in experiments 53-105. We are approximately 60% through these first 106 experiments and if preliminary analysis of the second set of experiments proves our hypothesis correct, we may choose to end the second set of simulations before completion in order to move on to new batches, all using the better simulation scheme.

Furthermore, while you’ve been crunching our work units without replication (quorum of 1), we designed the batches to have built in redundancy — which means that research tasks are assigned more than once in order to compare the results and confirm their accuracy — which we now conclude is too conservative. It is evident from analysis of the first set of batches that the current simulation protocols can be scaled down for future batches, allowing us to simulate more complexes at once on World Community Grid moving forward. We are currently preparing the next set of batches using docking results of more complexes from the SAMPL4 challenge which we recently received from the MGL laboratory at Scripps.

We anticipate that this first year of FightAIDS@Home Phase 2 will be extremely rewarding for our group and collaborators at the HIVE Center, and we’re very grateful for having been given this opportunity by IBM, and most importantly, World Community Grid volunteers.

It has also been an exciting month for the Levy lab. It’s our pleasure to announce that the January issue of Protein Science is a special issue in recognition of Ronald Levy’s contributions to the field of computational biophysics! The issue is free to read online. Professor Ron Levy, who designed the BEDAM tool used in this phase of the project, leads the molecular simulations in Phase 2 and we are very happy to help celebrate his accomplishments in this field.

See the full article here.

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“World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

WCG projects run on BOINC software from UC Berkeley.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!

“Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

Please visit the project pages-
Outsmart Ebola together

Mapping Cancer Markers

Uncovering Genome Mysteries

Say No to Schistosoma

GO Fight Against Malaria

Drug Search for Leishmaniasis

Computing for Clean Water

The Clean Energy Project

Discovering Dengue Drugs – Together

Help Cure Muscular Dystrophy

Help Fight Childhood Cancer

Help Conquer Cancer

Human Proteome Folding

FightAIDS@Home

World Community Grid is a social initiative of IBM Corporation
IBM Corporation

IBM – Smarter Planet

From Scripps: “Getting closer to an HIV Vaccine”

Scripps Research Institute

January 2016
No writer credit found

Authors of the new paper [no paper reference in article] included (left to right) James Voss, Raiees Andrabi, Dennis Burton, Bryan Briney and Chi-Hui Liang.

For more than 30 years, an effective vaccine against HIV has eluded scientists, and more than two million people are still newly infected with the virus each year. In a recent study, scientists at The Scripps Research Institute gained a new weapon in that long fight. They identified four antibodies targeting a specific weak spot on HIV that provided key information for the design of a potential HIV vaccine candidate.

“This study [no paper reference in article]is an example of how we can learn from natural infection and translate that information into vaccine development,” said TSRI Research Associate Raiees Andrabi. “This is an important advance in the field of antibody-based HIV vaccine development.”

Dr. Andrabi served as first author of the study, working in the lab of senior author TSRI Professor Dennis R. Burton, who is also scientific director of the International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center and of the National Institutes of Health’s Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID) at TSRI.

The findings build on the success of several recent TSRI studies showing that, with prompting, the immune system can develop antibodies to neutralize many strains of HIV. In the new study, the researchers carried out a series of experiments involving virus modifications and protein and antibody engineering. They found that four antibodies targeted a single spot on HIV’s surface called the V2 apex. This was significant because the V2 apex could be recognized by these antibodies on about 90 percent of known HIV strains – and even related strains that infect other species, meaning a vaccine that targets this region could protect against many forms of the virus.

“This region helps stabilize the virus, so it’s an important area to target if you want to neutralize HIV,” said Dr. Andrabi.

Investigating further, the researchers noticed that two of the four antibodies had an unusual feature that could prove important in vaccine design. The immune system usually begins its fight against infection by activating immune B cells that express “germline” forms of antibodies on their surface to bind invading pathogens. Germline antibodies rarely bind viruses very effectively themselves; instead, they are precursors for more developed antibodies, which mutate and hone their response to the invader.

Yet in the new study, two of the antibodies did not need to mutate to bind with the V2 apex; instead, these antibodies used part of their basic germline structure, encoded by non-mutated genes. This means any patient with HIV should, in theory, have the ability to kick-start the right immune response.

To generate that response, it was critical for the scientists to find the right proteins in HIV that the antibodies could recognize and bind to. In the new study, the researchers succeeded in mimicking a structure on HIV called the native HIV coat protein. This enabled them to design proteins that do indeed bind well to the germline antibodies and hopefully start a useful immune response. The next step will be to test the vaccine candidates in animal models.

See the full article here .

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The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

From UC Davis: “Turning the Tables on Hidden HIV”

Thirty years ago, contracting HIV was a death sentence.

The virus attacks the immune system, specifically T-cells, until immunity breaks down completely. Patients would eventually develop AIDS, and ultimately succumb to opportunistic infections.

The development of highly active antiretroviral therapies or HAART changed all that, converting a deadly disease into a chronic one. As long as patients stayed on the drug regimen, they could live normal lifespans. Their immune systems would recover and viral levels would decline to nearly zero.

But there’s a catch. Nearly zero is not the same as zero. HIV has a latency mode, during which the virus is dormant – evading both HAART and the body’s immune system. Remove HAART treatment, and the virus comes roaring back.

That means a lifetime consuming powerful and expensive treatments – if one’s body and health status can tolerate them in the first place. And no one knows how the drugs will affect patients after 20, 30 or 40 years.

“We’ve made great progress, but at the end of the day you still have more than 30 million people living with HIV,” says Satya Dandekar, professor and chair of the UC Davis Department of Medical Microbiology and Immunology. “Without drugs, the virus can come back at the same threat level for patients.

“Actually eradicating HIV is extremely critical.”

For decades, UC Davis researchers have worked with that ultimate goal in mind. Scientists have learned important details about how HIV operates along the way; for example, that it first attacks immune cells in the gut.

But now we’ve reached a new stage in the battle against HIV. The goal is no longer to control the disease, but to cure it. Two UC Davis groups are beginning clinical trials in hopes of doing just that.

Shock and kill

It would be hard to overstate the significance of HIV latency. The virus’s ability to evade treatment has made it difficult, if not impossible, to cure. The challenge for clinicians is to identify a two-pronged strategy: shock the latent virus out of hibernation, and hit it with immune treatments to kill it.

No image credit found

Dandekar, along with dermatologist Emanual Maverakis, are about to test the first part of that strategy. Just a few months ago, the Dandekar lab identified several agents that “wake up” HIV. One in particular, PEP005, has shown striking results. Even better, the drug is already approved by the U.S. Food and Drug Administration.

“We found this was really effective at reactivating HIV and works beautifully with other latency reactivating agents,” says Dandekar. “The thing that’s really exciting is that the molecule is in the drug PICATO, which treats skin cancer. It’s already approved and being used by patients.”

Now the UC Davis group hopes to extend PICATO’s uses to attacking HIV latency as well, and is launching a small clinical trial to test the drug’s safety in HIV patients. If the trial is successful, the team hopes to combine PICATO, and other drugs that reactivate HIV, with immunotherapies that would destroy the virus as it comes out of hiding.

“It will have to be a combination,” says Dandekar. “Just reactivating HIV from latency won’t be enough. We need to position the patient so those reactivated cells can be cleared.”

Reboot the system

UC Davis researchers are moving another promising approach into clinical trials as well. It involves taking blood stem cells from patients, genetically engineering them with anti-HIV genes, and returning them to the patients – essentially “rebooting” their immune systems and empowering them to eradicate or adequately suppress remaining HIV on their own over the long term.

“We are using our understanding of basic HIV biology to engineer each patient’s own stem cells to fight the virus,” says Joseph Anderson, an assistant adjunct professor who researches infectious diseases at the UC Davis Institute for Regenerative Cures, the university’s main stem cell research center. “We’re hoping that by reintroducing these cells in a bone marrow transplant, we can rebuild the immune system to resist HIV.”

Anderson and Mehrdad Abedi, a hematology professor and stem cell transplant specialist, are trying to replicate the treatment that cured Timothy Brown, also known as the “Berlin Patient.” Brown received a stem cell transplant from a donor whose genome contained an HIV-resistant mutation. That was seven years ago – and Brown remains HIV-free.

Anderson, who has been investigating anti-HIV genes since he was a Ph.D. student, is using three different genes to attack the virus, each one hitting a different mechanism associated with HIV infection. Like the drug cocktails used for HAART, multiple attack vectors may reduce the virus’s ability to evade treatment.

But a new key to the UC Davis team’s gene therapy strategy is also an improved viral vector that Anderson developed to help boost the treatment’s potency. The vector contains a gene that “tags” the surface of the stem cells that are HIV-resistant, allowing researchers to maximize their volume and potential power by culling out non-resistant cells before transplantation.

Anderson and Abedi have received an $8.5 million grant from the state’s stem cell agency, the California Institute for Regenerative Medicine or CIRM, to conduct the trial. The study will test the engineered stem cells in patients with HIV-related lymphoma, since they already require bone marrow transplants to treat their cancer. This trial will also test the therapy’s safety.

The team hopes the treatment will be a complete cure, but even a partial response would be great news for HIV patients.

“Maybe we won’t be able to eradicate it in some patients,” said Anderson, “but hopefully we are giving them enough of an HIV-resistant immune system that they can live the rest of their lives without having to take the antiretroviral drugs.”

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The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

From Brown: “Team describes rapid, sensitive test for HIV mutations”

Brown University

October 15, 2015
David Orenstein
david_orenstein@brown.edu
401-863-1862

RNA reconnaissance
A Brown team has developed a new method for analyzing the the RNA (green strands) of HIV for mutations (red dot) that convey drug resistance. The system does not require transcription of RNA to DNA, as current technologies do, and works. Image: Lei Zhang/Brown University

Tests that can distinguish whether HIV-positive people are infected with a drug-resistant strain or a non-resistant strain allow patients to get the most effective treatment as quickly as possible. In the November edition of the Journal of Molecular Diagnostics, a team of Brown University researchers describes a new method that works faster and more sensitively in lab testing than the current standard technologies.

The main advance enabling that improved performance is that the system operates directly on the virus’ more readily available RNA rather than requiring extra, potentially error-prone steps to examine DNA derived from RNA. In a single tube, the system can first combine two engineered probes (ligation) if a mutation is present and then make many copies of those combined probes (amplification) for detection.

“LRA (ligation on RNA amplification) uniquely optimizes two enzymatic reactions — RNA-based ligation, and quantitative PCR (polymerase chain reaction) amplification — into a single system,” said Anubhav Tripathi, professor of engineering at Brown and corresponding author on the paper. “Each HIV contains about 10,000 nucleotides, or building blocks, in its genetic material, and a drop of blood from a patient with resistant HIV can contain thousands to millions of copies of HIV. To find that one virus, out of thousands to millions, which is mutated at just a single nucleotide is like finding a needle in a haystack.”

The experiments reported in the paper show that the LRA test was sensitive enough to find a commonly sought K103N mutation in concentrations as low as one mutant per 10,000 strands of “normal” viral RNA. The LRA detection worked within two hours, while alternative technologies such as ASPCR or pyrosequencing, can take as long as eight.

LRA works by sending in many copies of a pair of short engineered probes of genetic material to complement the RNA in the HIV sample. Under optimized conditions, those pairs that perfectly match the target HIV RNA containing a mutation that causes drug resistance can rapidly become fused together, or ligated, by an enzyme. If there is a single nucleotide difference, the pair won’t fuse.

The fusing of the engineered genetic probes is designed to happen at room temperature. After a short period, the LRA system then heats the slightly alkaline solution, which shuts off the fusing reaction but turns on the amplification (copying) of fused pairs. That allows the LRA system to produce a strong signal of fused pairs, if there are any. All this happens in a single step, without any need to change solution.

Aiming for the clinic

The development of LRA is the product of a collaboration led by Tripathi and Dr. Rami Kantor, associate professor of medicine in the Warren Alpert Medical School. Kantor, who is also an HIV specialist at The Miriam Hospital and co-senior author of the paper, works in developing nations such as Kenya and India, monitoring HIV resistance. One day when Tripathi was at the Lifespan/Tufts/Brown Center for AIDS Research Retrovirology Core Laboratory to discuss his work, Kantor suggested a collaboration with the end goal of developing a cheap, quick and accurate HIV drug resistance mutation detection system for use in developing nations.

“We met soon thereafter and started working together on various developments and implementations of the ideas and on the integration of our worlds,” Kantor said.

The authors acknowledge in the paper that what they demonstrate, while successful in the lab, is clearly not ready for deployment in the field. The lab tests, for example, are shown to work on HIV RNA derived from plasmids, laboratory viral strains, not on samples from circulating viruses found in ailing patients. The RNA fragments were prepared in Kantor’s lab by Dr. Mia Coetzer, assistant professor of medicine and a co-author on the paper.

“The next steps are to continue the development of LRA and other methods on patient samples to detect additional mutations and address specific HIV challenges related to mutation detection, such as enormous genomic diversity,” Kantor said, “and work on incorporation of such methods onto a point-of-care device that would satisfy the infrastructure and low-cost needs of resource limited settings.”

Lei Zhang, a biomedical engineering graduate student in Tripathi’s lab is the lead author on the paper. In addition to Zhang, Coetzer, Tripathi, and Kantor, the paper’s other authors are Jingjing Wang (now at PerkinElmer) and Stephanie Angione (now at Massachusetts General Hospital). within one solution (purple droplet).

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Welcome to Brown

Located in historic Providence, Rhode Island and founded in 1764, Brown University is the seventh-oldest college in the United States. Brown is an independent, coeducational Ivy League institution comprising undergraduate and graduate programs, plus the Alpert Medical School, School of Public Health, School of Engineering, and the School of Professional Studies.

With its talented and motivated student body and accomplished faculty, Brown is a leading research university that maintains a particular commitment to exceptional undergraduate instruction.

Brown’s vibrant, diverse community consists of 6,000 undergraduates, 2,000 graduate students, 400 medical school students, more than 5,000 summer, visiting and online students, and nearly 700 faculty members. Brown students come from all 50 states and more than 100 countries.

Undergraduates pursue bachelor’s degrees in more than 70 concentrations, ranging from Egyptology to cognitive neuroscience. Anything’s possible at Brown—the university’s commitment to undergraduate freedom means students must take responsibility as architects of their courses of study.

From AAAS: “AIDS pioneer finally brings AIDS vaccine to clinic”

AAAS

8 October 2015
Jon Cohen

HIV’s gp120 (brown triangle) docking onto a CD4 receptor (grey finger) that studs a white blood cell. Subramaniam Lab/CCR/NCI/NIH. © 2014 Veronica Falconieri.

Human trials of more than 100 different AIDS vaccines have taken place since researchers proved in 1984 that HIV caused the disease. Robert Gallo, whose U.S. National Cancer Institute laboratory published the four landmark papers in Science that convinced the world of the link between this recently discovered retrovirus and the growing epidemic, has closely monitored—and often sharply critiqued—the AIDS vaccine search since it began. But Gallo, who now runs the Institute of Human Virology (IHV) in Baltimore, Maryland, has always been a spectator—until today.

Gallo’s team has been developing a vaccine with an unusual method of protection for 15 years and is now launching the first clinical trial of it in collaboration with Profectus BioSciences, a biotech that spun off from IHV recently. Known as a phase I study, the trial expects to enroll 60 people and will simply assess safety and immune responses of the full-length single chain vaccine. “It’s a terrible name,” says Gallo, who is not one to mince words.

The vaccine contains a version of HIV’s surface protein, gp120, engineered so that it links to a few portions of a protein called the CD4 receptor. When HIV infects cells, gp120 first binds to the CD4 receptor on white blood cells and then “transitions” in such a way that hidden parts of the virus are exposed, allowing it to bind to a second receptor on the immune cells called CCR5. Once bound to both receptors, HIV can enter the white blood cell and establish an infection. The IHV vaccine aims to generate antibodies that bind to HIV’s gp120 when it’s in this transitional state, ultimately blocking attachment to CCR5, aborting the infection process. The development of the vaccine is being led by IHV’s George Lewis, whose team includes Antonio DeVico and Timothy Fouts.

Gallo, 78, says it has taken a long time to move this vaccine into the clinic because he and his group have done extensive testing in monkeys, faced the typical vaccine challenges of manufacturing a human-grade product, and have had to scramble for funding. “Was anything a lack of courage?” asks Gallo, who frequently asks and answers his own questions. “Sure. We wanted more and more answers before going into people.”

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The American Association for the Advancement of Science is an international non-profit organization dedicated to advancing science for the benefit of all people.

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From COSMOS: “The virus that could help stop HIV”

COSMOS

5 Oct 2015
Viviane Richter

Researchers are starting to unravel the secrets of a virus that not only doesn’t make you sick, but can help you fight off other diseases.

Macaque monkeys can become infected with the primate version of the pegivirus Credit: egortupikov/gettyimages

We’ve all heard of friendly bacteria, but a friendly virus? Called the pegivirus, catching it doesn’t make you sick. Instead, it can help the immune system to keep HIV infections in check. Discovered in 1995, scientists do not understand how it works, but that could soon change. Researchers at the Wisconsin National Primate Research Centre recently discovered baboons have their own pegivirus strain, offering a new way to study the oddball virus. Their investigation, published in Science Translational Medicine in September, may inspire new ways to tackle HIV.

The pegivirus is found in about one in every six people, with infections lasting up to a decade before being cleared from the body. It can be transmitted from mother to child, through contact with an infected person’s blood, or sexually. In the US, where the virus is not included in routine blood bank screens, an estimated 1,000 people receive pegivirus-positive blood or blood products each day.

While the pegivirus is genetically related to the hepatitis C virus, it doesn’t cause disease. On the contrary, researchers discovered in 2001 that the pegivirus appeared to protect some HIV-positive patients from developing AIDS. An 11-year study of 362 patients found 56% of HIV-positive people who did not carry pegivirus died. But among those patients infected with the pegivirus, the death rate was only 29%.

How pegivirus thwarts HIV “has really been a bit confusing”, says Stephen Kent, an immunologist at the University of Melbourne. “But if you could mimic that with something that’s more potent – that would be good.”

So what’s the pegivirus’ secret? “That’s the million-dollar question,” says Adam Bailey, lead author of the new study. Researchers need to study the pegivirus in an animal before it can be answered – one where the virus behaves much as it does in humans, happily cohabiting with its host without causing disease. Macaques failed the test: after being given human pegivirus they quickly cleared the infection. Maybe it was a matter of finding a money-version of the virus? Primates are known to carry viruses closely related to those we carry. For instance many primate species carry a virus closely related to HIV, called Simian Immunodeficiency Virus (SIV)
.

So Bailey’s team hunted for a pegivirus that had struck up a long-term relationship with a non-human primate. They found it in 30-year-old samples of baboon blood stashed in a colleague’s freezer. Although that virus was genetically similar to the human strain, when it was injected into macaques it stayed in their blood for up to 200 days without causing harm, long enough for the researchers to study it.

The researchers euthanised some infected monkeys, analysed their tissues for pegivirus RNA, and found most of the virus nestled in the spleen and bone marrow. These are also the tissues where HIV holes up. Pegivirus appeared to be actively replicating only in bone marrow, since removing the spleen of an infected monkey did not change the blood levels of the virus.

The fact that pegivirus and HIV are replicating in the same tissues – though not necessarily in the same cells – offers a further a clue to how pegivirus may thwart HIV, says the study’s senior author, David O’Connor.

When the immune system detects an invading virus, it pumps out more T cells – the infantry of the immune army. Alas that strategy plays right into the enemy’s hands since HIV replicates in and destroys those very cells. More T cells are produced to make up the casualties, giving HIV more cells to exploit. This vicious cycle decimates the immune system.

Cell infected with HIV. HIV attacks T cells, which are crucial in the body’s immune system. The pegivirus helps the body resist HIV.Credit: THOMAS DEERINCK / NCMIR / getty images

The researchers found pegivirus seems to slow the recruitment of new T cells from bone marrow. Kent speculates the pegivirus might prompt T cells to make molecules that lock HIV out. For instance the anti-HIV drug Maraviroc acts this way by blocking the CCR5 receptor on T cells.

The Wisconsin team’s next step will be to co-infect macaques with pegivirus and SIV, the monkey form of HIV, to see how the viruses interact. They hope that once they discover how the pegivirus blocks HIV, they’ll be able to mimic the action with a drug.

Today’s antiretroviral drugs are good at keeping HIV at bay – it’s estimated they’ve lowered the number of HIV deaths by two-thirds. But as O’Connor says “there’s a lot of space to help people even further”

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