Stuck On Flu

Researchers at the University of California, San Diego School of Medicine have shown for the first time how influenza A viruses snip through a protective mucus net to both infect respiratory cells and later cut their way out to infect other cells.

 

In this cartoon, experimental magnetic beads are coated with human or pig mucins (grey mesh), which are proteins containing sialic acids (red or blue diamonds), part of a protective mucus net secreted by respiratory cells. Humans and pigs have different sialic acids on their mucins, as indicated by the bottom molecular structures. The flu virus (green stars) bind to and cleave off sialic acids, snipping through the host mucus net to infect cells. (Credit: UC San Diego Health System)

 

The findings, published online in Virology Journal by principal investigator Pascal Gagneux, PhD, associate professor in the Department of Cellular and Molecular Medicine, and colleagues, could point the way to new drugs or therapies that more effectively inhibit viral activity, and perhaps prevent some flu infections altogether.
Scientists have long known that common strains of influenza specifically seek and exploit sialic acids, a class of signaling sugar molecules that cover the surfaces of all animal cells. The ubiquitous H1N1 and H3N2 flu strains, for example, use the protein hemagglutinin (H) to bind to matching sialic acid receptors on the surface of a cell before penetrating it, and then use the enzyme neuraminidase (N) to cleave or split these sialic acids when viral particles are ready to exit and spread the infection.
Mucous membrane cells, such as those that line the internal airways of the lungs, nose and throat, defend themselves against such pathogens by secreting a mucus rich in sialic acids -- a gooey trap intended to bog down viral particles before they can infect vulnerable cells.
"The sialic acids in the secreted mucus act like a sticky spider's web, drawing viruses in and holding them by their hemagglutinin proteins," said Gagneux.
Using a novel technique that presented viral particles with magnetic beads coated with different forms of mucin (the glycoproteins that comprise mucus) and varying known amounts of sialic acids, Gagneux and colleagues demonstrated that flu viruses counteract the natural barrier by also using neuraminidase to cut themselves free from binding mucosal sialic acids.
More notably, he said that by blocking neuraminidase activity in the mucus, the viruses remain stuck. "They can't release themselves from the mucus decoy and thus can't infect."
The discovery is likely to alter the way researchers and pharmaceutical companies think about how viruses and flu therapies function. Existing drugs like Tamiflu and Relenza inhibit neuraminidase activity and presumably dampen the ability of the flu virus to spread among cells. The work by Gagneux and colleagues suggests inhibiting neuraminidase activity in mucus may reduce the initial risk of infection.
The challenge will be to restrict neuraminidase inhibition to the mucus. Many types of cells in the human body produce neuraminidases, each performing vital cellular functions, particularly in the brain. Limiting neuraminidase inhibition to relevant mucus-secreting cells is necessary to reducing potential side effects.
"The airway's mucus layer is constantly being shed and renewed, within a couple of hours the entire layer is replaced by a new layer," said first author Miriam Cohen, PhD, an assistant project scientist in Gagneux's lab. "A drug or compound that slows down neuraminidase activity rather than completely inhibit its activity will suffice to enhance the natural protective effect of mucus and prevent infection."
 

Journal Reference:

1. Miriam Cohen, Xing-Quan Zhang, Hooman P Senaati, Hui-Wen Chen, Nissi M Varki, Robert T Schooley, Pascal Gagneux. Influenza A penetrates host mucus by cleaving sialic acids with neuraminidase. Virology Journal, 2013; 10 (1): 321 DOI: 10.1186/1743-422X-10-321

Courtesy: ScienceDaily
 

How Flu Evolves to Escape Immunity

Scientists have identified a potential way to improve future flu vaccines after discovering that seasonal flu typically escapes immunity from vaccines with as little as a single amino acid substitution. Additionally, they found these single amino acid changes occur at only seven places on its surface -- not the 130 places previously believed. The research was published today, 21 November, in the journal Science.

 Family with the flu. Scientists have identified a potential way to improve future flu vaccines after discovering that seasonal flu typically escapes immunity from vaccines with as little as a single amino acid substitution. (Credit: © Creativa / Fotolia)

"This work is a major step forward in our understanding of the evolution of flu viruses, and could possibly enable us to predict that evolution. If we can do that, then we can make flu vaccines that would be even more effective than the current vaccine," said Professor Derek Smith from the University of Cambridge, one of the two leaders of the research, together with Professor Ron Fouchier from Erasmus Medical Center in The Netherlands.

The flu vaccine works by exposing the body to parts of inactivated flu from the three major different types of flu that infect humans, prompting the immune system to develop antibodies against these viruses. When exposed to the actual flu, these antibodies can eliminate the flu virus.

However, every two or three years the outer coat of seasonal flu (made up of amino acids) evolves, preventing antibodies that would fight the older strains of flu from recognising the new strain. As a result, the new strain of virus escapes the immunity that has been acquired as a result of earlier infections or vaccinations. Because the flu virus is constantly evolving in this way, the World Health Organisation meets twice a year to determine whether the strains of flu included in the vaccine should be changed.

For this study, the researchers created viruses which had a variety of amino acid substitutions as well as different combinations of amino acid substitutions. They then tested these viruses to see which substitutions and combinations of substitutions caused new strains to develop.

They found that seasonal flu escapes immunity and develops into new strains typically by just a single amino acid substitution. Until now, it was widely believed that in order for seasonal flu to escape the immunity individuals acquire from previous infections or vaccinations, it would take at least four amino acid substitutions.

They also found that such single amino acid changes occurred at only seven places on its surface -- all located near the receptor binding site (the area where the flu virus binds to and infects host cells). The location is significant because the virus would not change so close to the site unless it had to, as that area is important for the virus to conserve.

"The virus needs to conserve this, its binding site, as it uses this site to recognize the cells that it infects in our throats," said Bjorn Koel, from Erasmus Medical Center in The Netherlands and lead author of the paper.

Seasonal flu is responsible for half a million deaths and many more hospitalizations and severe illnesses worldwide every year.

Journal Reference:

1. Björn F. Koel, David F. Burke, Theo M. Bestebroer, Stefan Van Der Vliet, Gerben C. M. Zondag, Gaby Vervaet, Eugene Skepner, Nicola S. Lewis, Monique I. J. Spronken, Colin A. Russell, Mikhail Y. Eropkin, Aeron C. Hurt, Ian G. Barr, Jan C. De Jong, Guus F. Rimmelzwaan, Albert D. M. E. Osterhaus, Ron A. M. Fouchier, Derek J. Smith. Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution. Science, 22 November 2013: Vol. 342 no. 6161 pp. 976-979 DOI: 10.1126/science.1244730

Courtesy: ScienceDaily

Neanderthal Viruses Found in Modern Humans

Ancient viruses from Neanderthals have been found in modern human DNA by researchers at Oxford University and Plymouth University.

Scanning electron micrograph showing human immunodeficiency virus (spherical) on human lymphocytes. Researchers hope to further investigate ancient endogenous retroviruses, belonging to the HML2 family of viruses, for possible links with cancer and HIV. (Credit: CDC/C. Goldsmith, P. Feorino, E. L. Palmer, W. R. McManus)

The researchers compared genetic data from fossils of Neanderthals and another group of ancient human ancestors called Denisovans to data from modern-day cancer patients. They found evidence of Neanderthal and Denisovan viruses in the modern human DNA, suggesting that the viruses originated in our common ancestors more than half a million years ago.
This latest finding, reported in Current Biology, will enable scientists to further investigate possible links between ancient viruses and modern diseases including HIV and cancer, and was supported by the Wellcome Trust and Medical Research Council (MRC).
Around 8% of human DNA is made up of 'endogenous retroviruses' (ERVs), DNA sequences from viruses which pass from generation to generation. This is part of the 90% of our DNA with no known function, sometimes called 'junk' DNA.
'I wouldn't write it off as "junk" just because we don't know what it does yet,' said Dr Gkikas Magiorkinis, an MRC Fellow at Oxford University's Department of Zoology. 'Under certain circumstances, two "junk" viruses can combine to cause disease -- we've seen this many times in animals already. ERVs have been shown to cause cancer when activated by bacteria in mice with weakened immune systems.'
Dr Gkikas and colleagues are now looking to further investigate these ancient viruses, belonging to the HML2 family of viruses, for possible links with cancer and HIV.
'How HIV patients respond to HML2 is related to how fast a patient will progress to AIDS, so there is clearly a connection there,' said Dr Magiorkinis, co-author of the latest study. 'HIV patients are also at much higher risk of developing cancer, for reasons that are poorly-understood. It is possible that some of the risk factors are genetic, and may be shared with HML2. They also become reactivated in cancer and HIV infection, so might prove useful as a therapy target in the future.'
The team are now investigating whether these ancient viruses affect a person's risk of developing diseases such as cancer. Combining evolutionary theory and population genetics with cutting-edge genetic sequencing technology, they will test if these viruses are still active or cause disease in modern humans.
'Using modern DNA sequencing of 300 patients, we should be able to see how widespread these viruses are in the modern population. We would expect viruses with no negative effects to have spread throughout most of the modern population, as there would be no evolutionary pressure against it. If we find that these viruses are less common than expected, this may indicate that the viruses have been inactivated by chance or that they increase mortality, for example through increased cancer risk,' said Dr Robert Belshaw, formerly of Oxford University and now a lecturer at Plymouth University, who led the research.
'Last year, this research wouldn't have been possible. There were some huge technological breakthroughs made this summer, and I expect we'll see even greater advances in 2014. Within the next 5 years, we should be able to say for sure whether these ancient viruses play a role in modern human diseases.'

Journal Reference:

1. Emanuele Marchi, Alex Kanapin, Matthew Byott, Gkikas Magiorkinis and Robert Belshaw. Neanderthal and Denisovan retroviruses in modern humans. Current Biology, 2013 DOI: 10.1016/j.cub.2013.10.028

Courtesy: ScienceDaily
 

Rare New Microbe Found in Two Spacecraft Clean Rooms

A rare, recently discovered microbe that survives on very little to eat has been found in two places on Earth: spacecraft clean rooms in Florida and South America.

 This microscopic image shows dozens of individual bacterial cells of the recently discovered species Tersicoccus phoenicis. This species has been found in only two places: clean rooms in Florida and South America where spacecraft are assembled for launch. Spacecraft clean rooms are one of the most thoroughly checked environments on Earth for what microbes are present. The monitoring provides an indication of what species might get into space aboard a spacecraft. The image includes a scale bar showing that each of the bacterial cells is about one micrometer, or micron, across (about 0.00004 inch). (Credit: NASA/JPL-Caltech)

Microbiologists often do thorough surveys of bacteria and other microbes in spacecraft clean rooms. Fewer microbes live there than in almost any other environment on Earth, but the surveys are important for knowing what might hitch a ride into space. If extraterrestrial life is ever found, it would be readily checked against the census of a few hundred types of microbes detected in spacecraft clean rooms.
The work to keep clean rooms extremely clean knocks total microbe numbers way down. It also can select for microbes that withstand stresses such as drying, chemical cleaning, ultraviolet treatments and lack of nutrients. Perversely, microbes that withstand these stressors often also show elevated resistance to spacecraft sterilization methodologies such as heating and peroxide treatment.
"We want to have a better understanding of these bugs, because the capabilities that adapt them for surviving in clean rooms might also let them survive on a spacecraft," said microbiologist Parag Vaishampayan of NASA's Jet Propulsion Laboratory, Pasadena, Calif., lead author of the 2013 paper about the microbe. "This particular bug survives with almost no nutrients."
This population of berry-shaped bacteria is so different from any other known bacteria, it has been classified as not only a new species, but also a new genus, the next level of classifying the diversity of life. Its discoverers named it Tersicoccus phoenicis. Tersi is from Latin for clean, like the room. Coccus, from Greek for berry, describes the bacterium's shape. The phoenicis part is for NASA's Phoenix Mars Lander, the spacecraft being prepared for launch in 2007 when the bacterium was first collected by test-swabbing the floor in the Florida clean room.
Some other microbes have been discovered in a spacecraft clean room and found nowhere else, but none previously had been found in two different clean rooms and nowhere else. Home grounds of the new one are about 2,500 miles (4,000 kilometers) apart, in a NASA facility at Kennedy Space Center and a European Space Agency facility in Kourou, French Guiana.
A bacterial DNA database shared by microbiologists worldwide led Vaishampayan to find the match. The South American detection had been listed on the database by a former JPL colleague, Christine Moissl-Eichinger, now with the University of Regensburg in Germany. She is first co-author of the paper published this year in the International Journal of Systematic and Evolutionary Microbiology identifying the new genus.
The same global database showed no other location where this strain of bacteria has been detected. That did not surprise Vaishampayan. He said, "We find a lot of bugs in clean rooms because we are looking so hard to find them there. The same bug might be in the soil outside the clean room but we wouldn't necessarily identify it there because it would be hidden by the overwhelming numbers of other bugs."
A teaspoon of typical soil would have thousands more types of microbes and billions more total microbes than an entire cleanroom. More than 99 percent of bacterial strains, as identified from DNA sequences, have never been cultivated in laboratories, a necessary step for the various types of characterization required to identify a strain as a new species.
Microbes that are tolerant of harsh conditions become more evident in clean room environments that remove the rest of the crowd.
"Tersicoccus phoenicis might be found in some natural environment with extremely low nutrient levels, such as a cave or desert," Vaishampayan speculated. This is the case for another species of bacterium (Paenibacillus phoenicis) identified by JPL researchers and currently found in only two places on Earth: a spacecraft clean room in Florida and a bore hole more than 1.3 miles (2.1 kilometers) deep at a Colorado molybdenum mine.
Ongoing research with Tersicoccus phoenicis is aimed at understanding possible ways to control it in spacecraft clean rooms and fully sequencing its DNA. Students from California State University, Los Angeles, have participated in the research to characterize the newly discovered species.
The California Institute of Technology, Pasadena, operates JPL for NASA.
 

Journal Reference:

1. P. Vaishampayan, C. Moissl-Eichinger, R. Pukall, P. Schumann, C. Sproer, A. Augustus, A. H. Roberts, G. Namba, J. Cisneros, T. Salmassi, K. Venkateswaran. Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments. International Journal of Systematic and Evolutionary Microbiology, 2012; 63 (Pt 7): 2463 DOI: 10.1099/ijs.0.047134-0

Courtesy: ScienceDaily
 

Researchers Regrow Hair, Cartilage, Bone, Soft Tissues: Enhancing Cell Metabolism Key to Tissue Repair

Young animals are known to repair their tissues effortlessly, but can this capacity be recaptured in adults? A new study from researchers at the Stem Cell Program at Boston Children's Hospital suggests that it can. By reactivating a dormant gene called Lin28a, which is active in embryonic stem cells, researchers were able to regrow hair and repair cartilage, bone, skin and other soft tissues in a mouse model.

This image shows tissue regrowth in adult mice (reactivated Lin28a gene). (Credit: Cell, Shyh-Chang et al.)

The study also found that Lin28a promotes tissue repair in part by enhancing metabolism in mitochondria -- the energy-producing engines in cells -- suggesting that a mundane cellular "housekeeping" function could open new avenues for developing regenerative treatments. Findings were published online by the journal Cell on November 7.
"Efforts to improve wound healing and tissue repair have mostly failed, but altering metabolism provides a new strategy which we hope will prove successful," says the study's senior investigator George Q. Daley, MD, PhD, director of Boston Children's Stem Cell Transplantation Program and an investigator with the Howard Hughes Medical Institute.
"Most people would naturally think that growth factors are the major players in wound healing, but we found that the core metabolism of cells is rate-limiting in terms of tissue repair," adds PhD candidate Shyh-Chang Ng, co-first author on the paper with Hao Zhu, MD, both scientists in the Daley Lab. "The enhanced metabolic rate we saw when we reactivated Lin28a is typical of embryos during their rapid growth phase."
Lin28, first discovered in worms, functions in all complex organisms. It is abundant in embryonic stem cells, expressed strongly during early embryo formation and has been used to reprogram skin cells into stem cells. It acts by binding to RNA and regulating how genes are translated into proteins.
To better understand how Lin28a promotes tissue repair, the researchers systematically looked at what specific RNAs it binds to. They initially had their sights on a tiny RNA called Let-7, which is known to promote cell maturation and aging.
"We were confident that Let-7 would be the mechanism," says Shyh-Chang. "But there was something else involved."
Specifically, the researchers found that Lin28a also enhances the production of metabolic enzymes in mitochondria, the structures that produce energy for the cell. By revving up a cell's bioenergetics, they found, Lin28a helps generate the energy needed to stimulate and grow new tissues.
"We already know that accumulated defects in mitochondrial metabolism can lead to aging in many cells and tissues," says Shyh-Chang. "We are showing the converse -- that enhancement of mitochondrial metabolism can boost tissue repair and regeneration, recapturing the remarkable repair capacity of juvenile animals."
Further experiments showed that bypassing Lin28a and directly activating mitochondrial metabolism with a small-molecule compound also had the effect of enhancing wound healing. This suggests the possibility of inducing regeneration and promoting tissue repair with drugs.
"Since Lin28 itself is difficult to introduce into cells, the fact that we were able to activate mitochondrial metabolism pharmacologically gives us hope," Shyh-Chang says.
Lin28A didn't universally induce regeneration in all tissues. Heart tissue showed little effect, and while the researchers were able to enhance the regrowth of finger tips in newborn mice, they could not in adults.
"Lin28a could be a key factor in constituting a healing cocktail," says Shyh-Chang, "but there are other embryonic factors that remain to be found."
 

Journal Reference:

1. Ng Shyh-Chang, Hao Zhu, T. Yvanka de Soysa, Gen Shinoda, Marc T. Seligson, Kaloyan M. Tsanov, Liem Nguyen, John M. Asara, Lewis C. Cantley, George Q. Daley. Lin28 Enhances Tissue Repair by Reprogramming Cellular Metabolism. Cell, 2013; 155 (4): 778 DOI: 10.1016/j.cell.2013.09.059

Courtesy: ScienceDaily
 

Novel Genetic Patterns May Make Us Rethink Biology and Individuality

Professor of Genetics Scott Williams, PhD, of the Institute for Quantitative Biomedical Sciences (iQBS) at Dartmouth's Geisel School of Medicine, has made two novel discoveries: first, a person can have several DNA mutations in parts of their body, with their original DNA in the rest -- resulting in several different genotypes in one individual -- and second, some of the same genetic mutations occur in unrelated people. We think of each person's DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human, and impact how we think about using forensic or criminal DNA analysis, paternity testing, prenatal testing, or genetic screening for breast cancer risk, for example. Williams' surprising results indicate that genetic mutations do not always happen purely at random, as scientists have previously thought.

Concept image. We think of each person's DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human. (Credit: © WavebreakMediaMicro / Fotolia)

His work, done in collaboration with Professor of Genetics Jason Moore, PhD, and colleagues at Vanderbilt University, was published in PLOS Genetics journal on November 7, 2013.
Genetic mutations can occur in the cells that are passed on from parent to child and may cause birth defects. Other genetic mutations occur after an egg is fertilized, throughout childhood or adult life, after people are exposed to sunlight, radiation, carcinogenic chemicals, viruses, or other items that can damage DNA. These later or "somatic" mutations do not affect sperm or egg cells, so they are not inherited from parents or passed down to children. Somatic mutations can cause cancer or other diseases, but do not always do so. However, if the mutated cell continues to divide, the person can develop tissue, or a part thereof, with a different DNA sequence from the rest of his or her body.
"We are in reality diverse beings in that a single person is genetically not a single entity -- to be philosophical in ways I do not yet understand -- what does it mean to be a person if we are variable within?" says Williams, the study's senior author, and founding Director of the Center for Integrative Biomedical Sciences in iQBS. "What makes you a person? Is it your memory? Your genes?" He continues, "We have always thought, 'your genome is your genome.' The data suggest that it is not completely true."
In the past, it was always thought that each person contains only one DNA sequence (genetic constitution). Only recently, with the computational power of advanced genetic analysis tools that examine all the genes in one individual, have scientists been able to systematically look for this somatic variation. "This study is an example of the type of biomedical research project that is made possible by bringing together interdisciplinary teams of scientists with expertise in the biological, computational and statistical sciences." says Jason Moore, Director of the iQBS, who is also Associate Director for Bioinformatics at the Cancer Center, Third Century Professor, and Professor of Community and Family Medicine at Geisel.
Having multiple genotypes from mutations within one's own body is somewhat analogous to chimerism, a condition in which one person has cells inside his or her body that originated from another person (i.e., following an organ or blood donation; or sometimes a mother and child -- or twins -- exchange DNA during pregnancy. Also, occasionally a person finds out that, prior to birth, he or she had a twin who did not survive, whose genetic material is still contained within their own body). Chimerism has resulted in some famous DNA cases: one in which a mother had genetic testing that "proved" that she was unrelated to two of her three biological sons.
Williams says that, although this was a small study, "there is a lot more going on than we thought, and the results are, in some ways, astoundingly weird."
Because somatic changes are thought to happen at random, scientists do not expect unrelated people to exhibit the same mutations. Williams and colleagues analyzed the same 10 tissue samples in two unrelated people. They found several identical mutations, and detected these repeated mutations only in kidney, liver and skeletal body tissues. Their research examined "mitochondrial DNA" (mtDNA) -- a part of DNA that is only inherited from the mother. Technically all women would share mtDNA from one common female ancestor, but mutations have resulted in differences. The importance of Williams' finding is that these tissue-specific, recurrent, common mutations in mtDNA among unrelated study subjects -- only detected in three body tissues -- are "not likely being developed and maintained through purely random processes," according to Williams. They indicate "a completely different model …. a decidedly non-random process that results in particular mutations, but only in specific tissues."
If our human DNA changes, or mutates, in patterns, rather than randomly; if such mutations "match" among unrelated people; or if genetic changes happen only in part of the body of one individual, what does this mean for our understanding of what it means to be human? How may it impact our medical care, cancer screening, or treatment of disease? We don't yet know, but ongoing research may help reveal the answers.
Christopher Amos, PhD, Director of the Center for Genomic Medicine and Associate Director for Population Sciences at the Cancer Center, says, "This paper identifies mutations that develop in multiple tissues, and provides novel insights that are relevant to aging. Mutations are noticed in several tissues in common across individuals, and the aging process is the most likely contributor. The theory would be that selected mutations confer a selective advantage to mitochondria, and these accumulate as we age." Amos, who is also a Professor of Community and Family Medicine at Geisel, says, "To confirm whether aging is to blame, we would need to study tissues from multiple individuals at different ages." Williams concurs, saying, "Clearly these do accumulate with age, but how and why is unknown -- and needs to be determined."
As more and better data become available from high-throughput genetic analyses and high-powered computers, researchers are identifying an increasing number of medical conditions that result from somatic mutations, including neurological, hematological, and immune-related disorders. Williams and colleagues are conducting further research to examine how diseases, other than cancer or even benign conditions, may result from somatic changes. Williams, Moore and Amos will employ iQBS's Discovery supercomputer for next-generation sequencing to process subjects' DNA data. Future analyses will include large, whole-genome sequencing of the data for the two individuals studied in the current report.
Williams explains, "We know that cancer is caused by mutations that cause a tumor. But in this work, we chose to study mutations in people without any cancer. Knowing how we accumulate mutations may make it easier to separate genetic signals that may cause cancer from those that accumulate normally without affecting disease. It may also allow us to see that many changes that we thought caused cancer do not in many situations, if we find the same mutations in normal tissues."
Just as our bodies' immune systems have evolved to fight disease, interestingly, they can also stave off the effects of some genetic mutations. Williams states that, "Most genetic changes don't cause disease, and if they did, we'd be in big trouble. Fortunately, it appears our systems filter a lot of that out."
Mark Israel, MD, Director of Norris Cotton Cancer Center and Professor of Pediatrics and Genetics at Geisel, says, "The fact that somatic mutation occurs in mitochondrial DNA apparently non-randomly provides a new working hypothesis for the rest of the genome. If this non-randomness is general, it may affect cancer risks in ways we could not have previously predicted. This can have real impact in understanding and changing disease susceptibility."

Journal Reference:

1. David C. Samuels, Chun Li, Bingshan Li, Zhuo Song, Eric Torstenson, Hayley Boyd Clay, Antonis Rokas, Tricia A. Thornton-Wells, Jason H. Moore, Tia M. Hughes, Robert D. Hoffman, Jonathan L. Haines, Deborah G. Murdock, Douglas P. Mortlock, Scott M. Williams. Recurrent Tissue-Specific mtDNA Mutations Are Common in Humans. PLoS Genetics, 2013; 9 (11): e1003929 DOI: 10.1371/journal.pgen.1003929

Courtesy: ScienceDaily

Yeast, Human Stem Cells Drive Discovery of New Parkinson's Disease Drug Targets

Using a discovery platform whose components range from yeast cells to human stem cells, Whitehead Institute scientists have identified a novel Parkinson's disease drug target and a compound capable of repairing neurons derived from Parkinson's patients.

A dual yeast and human stem cell discovery platform for Parkinson's disease: Investigations in simple baker's yeast cells brought to light abnormalities in Parkinson's patient neurons and identified genes and small molecules that correct them. Yeast chemical genetics identified the targeted pathway, conserved from yeast to human cells, of one such molecule. (Credit: Tom DiCesare/Whitehead Institute)

The platform -- whose effectiveness is described in dual papers published online this week in the journal Science -- could accelerate the discovery of drug candidates that address the underlying pathology of Parkinson's and other neurodegenerative diseases. Today, no such drugs exist.
Parkinson's disease (PD) and such neurodegenerative diseases as Huntington's and Alzheimer's are characterized by protein misfolding, resulting in toxic accumulations of proteins in the cells of the central nervous system. Cellular buildup of the protein alpha-synuclein, for example, has long been associated with PD, making this protein a seemingly appropriate target for therapeutic intervention.
In the search for compounds that might alter a protein's behavior or function -- such as that of alpha-synuclein -- drug companies often rely on so-called target-based screens that test the effect large numbers of compounds have on the protein in question in rapid, automated fashion. Though efficient, such an approach is limited by the fact that it essentially occurs in a test tube. Seemingly promising compounds emerging from a target-based screen may act quite differently when they're moved from the in vitro environment into a living setting.
To overcome this limitation, the lab of Whitehead Member Susan Lindquist has turned to phenotypic screens in which candidate compounds are studied within a living system. In Lindquist's lab, yeast cells -- which share the core cell biology of human cells -- serve as living test tubes in which to study the problem of protein misfolding and to identify possible solutions. Yeast cells genetically modified to overproduce alpha-synuclein serve as robust models for the toxicity of this protein that underlies PD.
"Phenotypic screens are probably underutilized for identifying drug targets and potential compounds," says Daniel Tardiff, a scientist in the Lindquist lab and lead author of one of the Science papers. "Here, we let the yeast tell us what is a good target. We let a living cell tell us what's critical for reversing alpha-synuclein toxicity."
In a screen of nearly 200,000 compounds, Tardiff and collaborators identified one chemical entity that not only reversed alpha-synuclein toxicity in yeast cells, but also partially rescued neurons in the model nematode C. elegans and in rat neurons. Significantly, cellular pathologies including impaired cellular trafficking and an increase in oxidative stress, were reduced by treatment with the identified compound. Enabled by the chemistry provided by Nate Jui in the Buchwald lab at MIT, Tardiff found that the compound was working by restoring functions mediated by a cellular protein critical for trafficking that was previously thought to be "undruggable."
But would these findings apply in human cells? To answer that question, husband-and-wife team Chee-Yeun Chung and Vikram Khurana led the second study published in Science to examine neurons derived from induced pluripotent stem (iPS) cells generated from Parkinson's patients. The cells and differentiated neurons (of a type damaged by the disease) were derived from patients that carried alpha-synuclein mutations and develop aggressive forms of the disease. To ensure that any pathology developed in the cultured neurons could be attributed solely to the genetic defect, the researchers also derived control neurons from iPS cells in which the mutation had been corrected.
Chung and Khurana used the wealth of data from the yeast alpha-synuclein toxicity model to clue them in on key cellular processes that became perturbed as patient neurons aged in the dish. Strikingly, exposure to the compound identified via yeast screens in Tardiff's study reversed the damage in these neurons.
"It was remarkable that the compound rescued yeast cells and patient neurons in similar ways and through the same target -- a target we would not have identified without yeast genetics to guide us," says Khurana, a postdoctoral scientist in the Lindquist lab and a neurologist at Massachusetts General Hospital who recruited patients for participation in this research. Khurana believes that the abnormalities discovered occur in the early stages of disease. If so, successful manipulation of the targets identified here might help slow or even prevent disease progression.
For the researchers involved, these findings are a bit of surprise. Because neurodegenerative disorders like PD are largely diseases of aging, modeling them in a culture dish using neurons grown from iPS cells has been thought to be exceedingly difficult, if not impossible.
"Many, ourselves included, were skeptical that we could find any important pathologies for a neurodegenerative disorder by reprogramming patient cells," says Chung, a Senior Research Scientist in the Lindquist lab. "Critically, we also validated these pathologies in post-mortem brains, so we're quite confident these are relevant for the disease."
Next steps for these scientists include chemically optimizing the compound identified and testing it in animal models. Moreover, they are convinced that this yeast-human stem cell discovery platform could be applied to other neurodegenerative diseases for which yeast models have been developed.
"Using yeast genetics to identify a compound and its mechanism of action against the fundamental pathology of a disease illustrates the power of the system we've built," says Lindquist, who is also professor of biology at MIT and a Howard Hughes Medical Institute investigator. "It's critical that we continue to leverage this power because as we reduce the rate at which people are dying from cancer and heart disease, the burden of these dreaded neurodegenerative diseases is going to rise. It's inevitable."
This work was supported by the National Institutes of Health (grants 5R01GM069530, GM58160, K01 AG038546, 5 R01CA084198), Howard Hughes Medical Institute, the JPB Foundation, the Eleanor Schwartz Charitable Foundation, the Bachmann-Strauss Dystonia & Parkinson Foundation, the American Brain Foundation, and the Parkinson's Disease Foundation.
 

Journal Reference:

1. Daniel F. Tardiff, Nathan T. Jui, Vikram Khurana, Mitali A. Tambe, Michelle L. Thompson, Chee Yeun Chung, Hari B. Kamadurai, Hyoung Tae Kim, Alex K. Lancaster, Kim A. Caldwell, Guy A. Caldwell, Jean-Christophe Rochet, Stephen L. Buchwald, Susan Lindquist. Yeast Reveal a “Druggable” Rsp5/Nedd4 Network that Ameliorates α−Synuclein Toxicity in Neurons. Science, 2013 DOI: 10.1126/science.1245321

Courtesy: ScienceDaily