How a plant molecule is a “superb” sunscreen

October 30, 2014 § Leave a comment

 

 

Plants make their own sunblock to protect against UV damage. Image from http://en.wikipedia.org/wiki/Plant#mediaviewer/File:Leaf_1_web.jpg

Like us, plants worry about sunburn. Research now shows that a molecule called sinapoyl malate found in plants is one hardworking sunblock. It captures some of the most damaging radiation from the sun.

Ultraviolet radiation is split into nine groups. One of the groups is UV-B radiation in the 280 to315 nm range. Overexposure to UV-B radiation in humans causes sunburn and some forms of skin cancer. In plants, the radiation can cause DNA damage and interfere with photosynthesis.

Timothy Zwier at Purdue University, who led the recent study published in the Journal of the American Chemical Society, says he got intrigued by sinapoyl malate when a Purdue colleague, Clint Chapple, discovered that the molecule was responsible for acting as a sunscreen in plants. While sinapoyl malate generally was known to absorb UV-B radiation in aqueous solution, the inherent spectral properties of the bare molecule were unknown.

Zwier’s lab’s specialty is studying the UV spectroscopy of isolated molecules in the gas phase. But the problem is that sinapoyl malate, like most other biological molecules, can’t be heated into a gas because it breaks down.

So Zwier and colleagues zapped the molecule off a thin film with a laser to get it into the gas phase. Once the molecule was in the gas phase, the investigators cooled it down to a temperature within a few degrees of absolute.

“This gave us a chance to study the inherent spectroscopic signatures of this UV-B-sunscreen molecule as an isolated molecule, free from the effects of solvent and cooled to low temperatures, where it can best reveal its secrets,” says Zwier.

However, sinapoyl malate had a surprise. Even in the stripped-down experimental conditions, the molecule’s spectrum was inherently broad, absorbing continuously over all wavelengths encompassed in the UV-B radiation range. Zwier notes that in its natural environment in the plant cell’s aqueous condition, sinapoyl malate probably works in conjunction with other factors to cover even more of the UV spectrum.

“Nevertheless, at the most fundamental quantum mechanical level, sinapoyl malate has what it takes to be a superb UV-B sunscreen — large absorption cross-section in the right wavelength range and complete spectral coverage,” says Zwier. “Nature has chosen a molecule to serve as its UV-B sunscreen that is extraordinarily well-suited for the task.”

Synchronizing mitochondrial metabolism

October 22, 2014 § Leave a comment

Seeing mitochondria go through waves of ATP production. Image by Roberto Weigert and Natalie Porat-Shliom.

Watching mitochondria go through waves of ATP production. Image by Roberto Weigert and Natalie Porat-Shliom.

Mitochondria are fidgeters. That’s what researchers discovered in a recent study. The organelles undergo waves in ATP production. Furthermore, the mitochondria, like synchronized dancers, work in a coordinated fashion.

A team at the National Institute of Dental and Craniofacial Research report in a paper just out in the journal Cell Reports that mitochondria in the salivary glands of live rats “undergo sustained and spontaneous metabolic oscillations under basal conditions,” says Roberto Weigert, who led the study. “Although we do not know why mitochondria adopt this oscillatory modality, we have speculated that this is the best way to rapidly respond to changes in energy demands.”

Weigert explains that the oscillations refer to periodic oscillations in ATP production. “When you image the mitochondria, it gives the impressions of a movement, but in reality they are physically steady,” he says.

The finding that mitochondria undergo oscillations in ATP production contradicts earlier reports that the phenomenon occurred only when cells in culture were stimulated. But Weigert and colleagues found that mitochondria in the acinar cells in the salivary tissues oscillate their energy output without any trigger for as long as tens of seconds to minutes. The oscillations were longer, faster and more frequent than observed previously in cell culture.

Furthermore, the investigators found that mitochondria synchronized their energy output throughout the entire tissue by relying on the activity of gap junctions.  “It was a real surprise to observe large areas of the salivary tissue ‘oscillating’ in a coordinated fashion,” says Weigert. “Our study underscores the role of the tissue environment in regulating and coordinating basic cellular processes in ways that are different from what is observed in reductionist model systems.”

To study mitochondria in tissues of live rodents, the investigators used a technique called subcellular intravital microscopy. The technique gave a readout of NADH, which is the substrate of complex I during oxidative phosphorylation in mitochondria, and TMRM, a cationic dye that shows the mitochondrial membrane potential.

Through other experiments, the investigators found that the metabolic oscillations were connected to the production of reactive oxygen species, which are a byproduct of ATP production in mitochondria.  The observation hints that the oscillations reflect the energy status of the cells.

Weigert says the team now is “interested in characterizing the machinery initiating and regulating the oscillations in the salivary glands.” He adds they want to extend their studies to other organs in order to establish how widespread is the process and to find how the oscillations are altered during high-energy processes or pathological conditions, such as cancer or metabolic diseases.

Sharing my byline and other adventures in punk rock

October 1, 2014 § 2 Comments

web-rotator-punksI gingerly slid the disc into my car CD player and braced myself against the steering wheel for the anticipated onslaught of noise. Instead, a voice, rich and smooth like molten chocolate, began to pour. With that, my introduction to The Offspring’s multiplatinum album “Smash,” and punk rock in general, began.

Up until that point, I had never listened to punk rock. But I had gotten myself into a situation where I needed to know enough about the genre so as not to embarrass myself.

The situation was a year in the making. Geoff Hunt, ASBMB’s public outreach coordinator, had told me and Angela Hopp, ASBMB Todays editor, about punk rockers who had science backgrounds. I had never heard of the musicians or the bands, but I love writing about people with off-the-beaten-path life stories. I grew excited at the thought of telling the stories of punk rockers who doubled as scientists.

But Geoff, a hardcore punk rock fan, threw me. “I’ll write the profiles,” he said. “I know the music.” Then he walked out of my office before I could speak up. As a journalist and writer, it’s my business to learn about new things and to quickly become expert enough to write stories that are in context and accurate. Geoff, I felt, was underestimating me.

A year went by, and Geoff, swamped with his many outreach projects, didn’t get the time to write the profiles. One day in early April, when I had just finished an intricate science feature and was ready to sink my teeth into something new, I pointed out to Angela on a whim that the punk rocker profiles still were waiting. “Geoff’s had a year, and he’s not done them. I can do them,” I recall stating brashly.

Angela went to see Geoff. I don’t know how the conversation went, but all I know is that Angela walked past my office later and said with a grin, “You two are going to co-write those profiles.”

My earlier brashness was now trumped by panic. I don’t mind feeling like an unsteady toddler when launching into a story in unfamiliar territory. But co-writing with Geoff meant that I had to be on par with him from the get-go, and, for the sake of my ego, I preferred that he not see my ungainly struggle with learning about punk rock.

I turned to Wikipedia (yes, that’s precisely how little I knew) and started to read about The Offspring, Descendents, and Bad Religion, the three bands whose lead singers are trained in science. Even the Wikipedia entries left me bewildered. I had to admit that I needed some guidance. A bit sheepishly, I asked Geoff if he could give me CDs to listen to while we waited for responses to our interview requests.

So that’s how I ended up with the CD of “Smash” and several others by Bad Religion and Descendents in my car. The CDs mingled with my own collection of the Beatles, Queen, Adele, P!nk, Motown, and my all-time favorite band, Duran Duran (a band that makes Geoff cringe). I was not exposed to punk rock while growing up in the Middle East. My Western pop music education was based on pirated copies of albums by top-selling mainstream artists and the British show “Top of the Pops.” I assumed punk rock to be like heavy metal, which I never found to be melodic. In my head, punk rock consisted of angry yelling into a microphone by a beefy guy with spiky rainbow hair and clothes with studs against the backdrop of thrashing drums about to go up in flames.

The musicality of “Smash” surprised me. In particular, I found myself drawn to the song “Gotta Get Away” and actually caught myself humming the tune. Bad Religion’s lyrics made me pay close attention and think. And as a singer, I loved Descendents’ Milo Aukerman’s vocal fry.

I wasn’t sure what to expect during the interviews with the three singers. I am a savvy interviewer of scientists, but this was my first time interviewing musicians. It didn’t help that I was dogged by the perception of the meathead punk rocker.

But I was so wrong. Aukerman was thoughtful and articulate. The Offspring’s Dexter Holland was charming and funny. Greg Graffin of Bad Religion was eloquent and sharp and insisted you choose your words carefully when speaking. All three were equally comfortable conversing about music and science in depth.

Truth be told, Geoff’s presence made all the difference during the interviews. He is steeped in the bands’ music and fan folklore, so he was able to ask questions that never would have occurred to me. Thanks to him, we got Holland to regale us with the story of how the hook “Keep ’em separated” in the song “Come Out and Play” came from a moment in the lab. That story turned into the lede of the profile we wrote about him.

But the co-writing process was bumpy. I had to bare my writing soul, which was very uncomfortable.

I am a firm believer in what Anne Lamott calls “shitty first drafts” in her book “Bird by Bird”. When beginning a fresh piece of writing, I do a brain dump of everything I know about the topic and then slowly begin the innumerable rounds of writing, cutting, rewriting and editing.

But Angela, knowing me all too well, warned me not to steamroll Geoff in my single-minded quest to get the final polished pieces. She specifically instructed me to give him room in the writing process. This, I realized with horror, meant that he was going to see my first drafts. Until this point, no one had ever read them.

Self-doubt is always a devil on my shoulder. I feared that Geoff would call me out as a lousy writer. I knew I could do several rounds of rewriting before giving him a draft to work on, but that would shut him out of the organic process of shaping the stories, the very thing Angela warned me not to do. When I hit “send” on the first draft about Holland, a small part of me died.

Naturally, quibbles flared up. Geoff was prone to references that only diehard punk fans would understand. There was a spat over whether the average ASBMB Today reader would understand a reference to The Ramones (it got to stay in the Graffin profile). Geoff disliked my terse news reporter style of writing; I pruned back his literary and long sentences. “There is so much tension in the writing!” Angela complained at one point, exhausted with having to referee two strong personalities.

With time, I grew comfortable writing with Geoff. I knew he was a reliable writer and, most importantly, a voracious reader. (I belong to the school that a good writer has to be a reader first.) But I was surprised at exactly how adept a writer he was. He shook me out of my own writing process, which had become more habit than craft, and forced me to experiment with language again. Playing with language reminded me afresh why I had become a writer in the first place.

Our profiles of Aukerman, Holland and Graffin went into a bigger series that we called, after much debate and some eye-rolling, “Defying Stereotypes.” The irony of the series name didn’t escape me. I had entered into this project with a set view of what punk rock was all about and what a punk rocker was supposed to be like. By introducing me to The Offspring, Descendents and Bad Religion, Geoff forced me to reevaluate my long-held perceptions.

Geoff even acted as my guide at my first punk rock concert this summer, when we went to see Bad Religion and The Offspring in Baltimore. But he may have regretted that one. On our drive back to Washington, D.C., after the concert, I burst into a mashup of the choruses of “Gotta Get Away” and Duran Duran’s “Rio.”

To read about Geoff’s take on writing the three profiles, go here. Also, speaking of the life-changing moments brought on by this experience, I would be remiss not to mention that I became acquainted with, and then seriously addicted to, Dexter Holland’s hot sauce, Gringo Bandito.

 

 

A mouse model for childhood obesity

September 18, 2014 § 1 Comment

 

Images of fetal and adult human adipose tissue grafted onto kidneys of immunodeficient mice. Photos were taken at the time of explantation at 14, 30 and 60 days  after transplantation. Yellow arrows indicate the position of grafts of human tissue. Scale bars are 2mm in length.

Images of fetal and adult human adipose tissue grafted onto kidneys of immunodeficient mice. Photos were taken at the time of explantation at 14, 30 and 60 days
after transplantation. Yellow arrows indicate the position of grafts of human tissue. Scale bars are 2mm in length.

Over the past 30 years, childhood obesity has more than doubled and teenage obesity has quadrupled. Researchers want to identify and understand the molecular triggers that set off children down the obesity path.  “There is considerable evidence that the prenatal environment can predispose the offspring to obesity. This is most clearly seen in children born to mothers who are overweight during pregnancy,” says Philip Gruppuso at Brown University. “However, there is not a suitable model to study human fat development.”

So to come up with such a model, Gruppuso, along with Jennifer Sanders at Brown University, led a team to create mice that carry human fetal fat tissue. As they report in a paper just out in the Journal of Lipid Research, these mice can be used to study human fat development.

The investigators took mid-gestation human fetal adipose tissue and implanted it into mice that were immunodeficient. This way, they avoided the problem of the animals rejecting the foreign tissue. The investigators were helped by Kim Boekelheide, also at Brown University, who developed the implantation technique.

Following a two-week period of latency after implantation, the transplanted human fat tissue began to develop steadily over two months. The tissue expressed genes associated with fat cell differentiation and development.

The investigators tried to do the same experiment with adult human fat tissue, but found that they couldn’t get the tissues to graft. The investigators suspect that the fetal tissue grew in the mice because the tissues were already programmed to develop new fat tissue and blood vessels.

The ultimate aim with these animals to is tease out which molecular factors trigger obesity to take hold in children. “Our goal is to manipulate the rodent hosts, for example with an altered diet or exposure to environmental toxicants, to examine the effect on the transplanted human tissue,” explains Gruppuso.

Surviving in the Pacific Ocean, bacterial style

September 4, 2014 § Leave a comment

Scientists collected samples during a research cruise in October 2011 along a 2,500-mile stretch in the Pacific Ocean, from Hawaii to Samoa. The transect cut across regions with widely different concentrations of nutrients, from areas rich in iron to the north to areas near the equator that are rich in phosphorus and nitrogen but devoid of iron. [Credit: Brian Dimento, University of Connecticut]

Scientists collected samples during a research cruise in October 2011 along a 2,500-mile stretch in the Pacific Ocean, from Hawaii to Samoa.
[Credit: Brian Dimento, University of Connecticut]

Oceans cover 70 percent of the earth’s surface. Given this vast area, how do you thoroughly study how a particular organism survives in it? In a paper just out in Science, researchers analyzed how a type of cyanobacteria ekes out an existence in a 2,500-mile stretch of the Pacific Ocean. The researchers were able to measure for the first time changes in absolute protein concentrations expressed by the community of this cyanobacterium as it weathered scarcities of different nutrients. In another paper in the same issue of Science, a different group of researchers focused on a particular enzyme that helps marine cyanobacteria and other microorganisms survive under conditions of nutrient deficiency and discovered what makes the enzyme tick.

The oceans harbor “much of Earth’s biological diversity,” points out Mak Saito at the Woods Hole Oceanographic Institution who was the first author on the first Science paper. Researchers want to know how the microorganisms, which are the foundation of the marine food web and are essential to the cycling of biologically important elements, survive in oceans. The researchers want to understand how changes in carbon, phosphorus, nitrogen and other elements, caused by natural means or human activity, affect the survival of these critical microorganisms.

But Saito says experiments to analyze the effects of nutrients on marine microorganisms are difficult to do and tend to only give a glimpse of what’s going on. So Saito’s group turned to proteomic technologies because they could use them to quantitatively study the details of the biochemical changes happening in the microorganisms across the Pacific Ocean. The investigators spent a month on a ship, traveling across the Central Pacific Ocean, from Hawaii to Samoa, and collecting microbial protein samples from as deep as 1 kilometer from the ocean. The path they traveled cut through the northern regions that were rich in iron to areas near the equator that were plentiful in phosphorus and nitrogen but lacked iron. For each sample, the investigators filtered  300-800 liters of seawater over 4-6 hours through 0.2-micron filters and froze the samples.

When they got back to Woods Hole, they used two different proteomic methods to study how the protein content changed in their samples that they took from the 2,500-mile stretch of the Pacific Ocean. Saito says that previous studies identified many proteins in the oceans and their relative abundances. In contrast, the measurements he and his colleagues carried out are the first quantitative marine protein concentration measurements “in units of femtomoles of protein per liter of seawater,” he says. “By measuring the concentrations of proteins, we can map changes in the microbial biochemistry across the ocean basin.”

From their data, Saito and colleagues showed that multiple nutrient scarcities affected the cyanobacterial community they chose to track. Their conclusion refutes the notion on which previous work in the field was based, which is microbial growth and protein production was at the mercy of a single nutrient that was scarcest.

Indeed, “biogeochemists have realised that the availability of more than one inorganic nutrient may simultaneously restrict growth of microorganisms, particularly if the concentrations of the nutrients are linked by biological processes,” says Ben Berks at the University of Oxford in the U.K. who led the team in the second Science paper that identified a critical cofactor for an alkaline phosphatase found in cyanobacteria and other microorganisms. The team on the second Science paper is unaffiliated with Saito’s team on the first Science paper.

The phosphatase, PhoX, was reported to be a calcium-dependent enzyme. “However, we noticed that the purified protein had a purple color and we knew this could not arise from calcium ions,” says Berks. “This observation prompted us to investigate the nature of the PhoX cofactor.”

Although PhoX activity is critical in many microorganisms, the enzyme has not been characterized in detail.  “Possibly it reflects the fact that, although the enzyme is widespread in environmental organisms, it is not present in commonly studied model organisms,” suggests Berks.

The investigators crystallized the enzyme and then used an X-ray spectroscopic technique called micro-PIXE as well as electron paramagnetic resonance spectroscopy to identify the metals that were a part of the enzyme. They identified an iron-calcium cofactor.

Previously PhoX was thought to be a simple calcium-dependent enzyme. Calcium is abundant in seawater. If calcium was readily available, Saito says, “people wondered how microbes were maintaining the PhoA zinc alkaline phosphatase.”

Zinc is a rare commodity in marine environments. Why would a microorganism go through the trouble of relying on zinc when there was plenty of calcium to spare for enzyme activity? Now that Berks and colleagues have shown that PhoX depends on iron and calcium to function, says Saito, it now becomes clear the microorganisms are forced to make do with two different scarce elements.

The discovery of a new enzyme cofactor also means that the work of marine biochemists has a long way to go. As Berks notes, “The work demonstrates that there are still novel biological cofactors to discover within the pool of currently unstudied microbial proteins.”

Model to explain cellular sensor organization

August 15, 2014 § Leave a comment

 

A new model proposes a general organizing principle for sensors on cells. Image from http://en.wikipedia.org/wiki/Cell_(biology)#mediaviewer/File:DAPIMitoTrackerRedAlexaFluor488BPAE.jpg

A new model proposes a general organizing principle for sensors on cells. Image from http://en.wikipedia.org/wiki/Cell_(biology)#mediaviewer/File:DAPIMitoTrackerRedAlexaFluor488BPAE.jpg

 

Cell-surface receptors are like radiowave antennae: They pick up signals to send them forward to the appropriate cellular equipment that process the information in the signals. But how do cells know where to best position receptors to cleanly and efficiently pick up the numerous signals coming at them?

In a paper recently published in the Proceedings in the National Academy of Sciences, Garud Iyengar at the Columbia University and Madan Rao at the Raman Research Institute and the National Centre for Biological Sciences in India came up with a theoretical model inspired by observations made in cell biology. They noted that different kinds of cell-surface molecules involved in sensing, such as receptors, share a common organizational motif. Sensors are either organized as dynamic clusters or as monomers. What was the organizing principle?

Iyengar and Rao used information theory to model how cells come up with an organizing principle for cell-surface receptors. In their model, cells must balance two contradictory needs. They must cluster some types of receptors at a given location to reduce the statistical `reading’ error but spread out other types of receptors across the cell surface. To figure out which ones to cluster and which ones to keep as monomers, cells assess the number of receptors they have at their disposal, how well the receptors function as sensors and how long it takes for the receptors to pick up signals in space and time.

The model by Iyengar and Rao predicts that receptors that bind to more than one ligand, and therefore are more susceptible to inadvertently picking up wrong ligands, are more likely to be clustered; receptors that selectively bind to one or two ligands roam freely on the cell surface.

Rao and Iyengar explains that the model doesn’t apply to just cellular organization of receptors. Rao says, “This research may have implications for many different contexts, from ad-hoc sensor networks to immunology.” The investigators point out that the distributions of integrins and E-cadherins in mammalian cells or the organization of receptors on bacteria for chemosensing may follow this model.

How a squid forms a relationship with a bacterium

July 28, 2014 § Leave a comment

The Hawaiian bobtail squid forms a symbiotic relationship with a bioluminescent bacterium. Photo provided by Spencer Nyholm.

The Hawaiian bobtail squid forms a symbiotic relationship with a bioluminescent bacterium. Photo provided by Spencer Nyholm.

How do you get into a mutually beneficial relationship? That is the question researchers asked in a recent paper in the journal Molecular & Cellular Proteomics, albeit for a squid and its bacterial partner. The researchers showed that in order for the Hawaiian bobtail squid to form a symbiotic relationship with the bioluminescent Vibrio fischeri, proteomic changes have to occur in a set of cells of the squid.

The Hawaiian bobtail squid, formally known as Euprymna scolopes, has a light organ that is exclusively colonized by V. fischeri. The squid feeds the bacterium a solution of sugar and amino acids and, in return for the steady food supply, the bacterium gives off the light that masks the squid’s silhouette while it goes hunting for various species of shrimp for its own meals.

Scientists study the squid and its bacterial partner as a model to understand how beneficial bacteria form associations with multicellular organisms and help animals develop. “Our lab is interested in understanding the role of the host’s innate immune system in establishing specificity,” says Tyler Schleicher at the University of Connecticut, the first author on the MCP paper. “Each generation of squid is colonized by V. fischeri from the environment, and they must distinguish between the symbiont and a huge background of nonsymbiotic bacteria that are found in seawater.” The question is how the squid achieves this feat.

To answer the question, the investigators used two quantitative proteomic techniques to compare a set of special cells taken from squid colonized with bacteria and those that were uncolonized. “This is the first time that two independent, high-throughput proteomic techniques have been applied to the squid-Vibrio association,” says Spencer Nyholm, also at the University of Connecticut, and the senior author on the paper.

The cells the investigators chose to look at are hemocytes, which are blood cells in the squid’s light organ; these cells have properties of the immune system’s macrophages and interact with the symbiotic bacteria present at the light organ.

From the investigators’ analyses of the differences in protein expression in hemocytes taken from colonized and uncolonized squid, they saw that the presence of V. fischeri in the light organ induced changes in the hemocyte proteome to promote the cell’s tolerance of the bacteria and favor symbiosis.  The changes involved the cytoskeleton, lysosome function, proteases and receptors.  Because scientists still don’t understand the precise mechanisms that contribute to host-symbiont specificity, the investigators are now focusing on studying several proteins identified in this study that appear to influence the bacterium’s adhesion to the squid’s light organ.

“A growing body of evidence from a variety of animal model systems suggests that beneficial microbes influence a host’s innate immune system to foster these associations,” says Nyholm. Because macrophagelike cells similar to hemocytes are found in almost all animals, he adds, “our study may provide insight into other host-microbe associations.”

On the hook: A new pipette to capture single cells

July 23, 2014 § Leave a comment

The handheld single-cell pipette. Image provided by Lidong Qin.

The handheld single-cell pipette. Image provided by Lidong Qin.

Seeking out individuals from a crowd has become increasingly important for biologists interested in single-cell analyses. Studies on individual cells allow scientists to understand processes that happen within this basic unit of life that often get masked by approaches that analyze groups of cells.

But there is “one very basic problem — how can one precisely pick up an individual cell?” asks Lidong Qin at the Houston Methodist Research Institute. Current methods of isolating single cells can be inefficient, expensive, time-consuming, biased or labor-intensive. Now, in a paper just out in the Journal of the American Chemical Society, Qin and colleagues describe a new kind of pipette specially designed to pick out single cells. “The pipette platform is almost a universal tool that is easy, cheap and reproducible,” says Qin.

The instrument, called the handheld single-cell pipette or hSCP, has dimensions much like a conventional handheld air-displacement pipette. It has two channels and one tip.

A researcher uses the hSCP to suck up cells from a Petri dish. Inside the pipette tip is a hook small enough to catch a single cell at random from the cells that get sucked up from the dish. Those cells that are not on the hook get removed by a flow of liquid, while the single cell on the hook can be deposited into standard 96-well or similar types of plates, Petri dishes or vials for single-cell biochemical analyses, such as cloning or the polymerase chain reaction.

Qin says the next priority is to develop the prototype into a device that can be mass-produced and commercialized.

Thalidomide’s molecular actions revealed

July 16, 2014 § Leave a comment

Once shunned for causing severe birth defects in babies, thalidomide has made a comeback to treat some blood cancers and leprosy. In a paper now out in Nature, researchers describe the crystal structure of the drug bound to its target. From their data, the researchers provide an explanation how this drug can either save or wreck lives.

In the 1950s, women in Europe and other parts of the world were given the sedative thalidomide to battle morning sickness. But shortly thereafter, physicians realized that drug, which was marketed by a German company, caused limb deformities and other developmental problems in children. In 1961, the drug was withdrawn from the market. Nicolas Thomä at Friedrich Miescher Institute for Biomedical Research in Switzerland says that the notorious side effects of thalidomide were impossible to ignore when he was a child. “Born in Germany in the 1970s, I saw the teratogenic side effects of thalidomide,” he says. “I come from a small community and grew up with children who were directly affected by the drug.”

So in 2010, when another group of researchers demonstrated that thalidomide binds to a protein that’s part of a ubiquitin ligase complex, Thomä was doubly intrigued. His group long has been interested in ubiquitin ligases. Furthermore, conventional thinking had dictated to date that ubiquitin ligases couldn’t be targeted by drugs. But here was thalidomide, binding to a protein called CRBN. CRBN is a ubiquitously expressed protein that is part of a family of ubiquitin ligase complexes called CRL4; mutations in CRBN are associated with mental retardation. In 1998, the U.S. Food and Drug Administration approved the use of the drug to treat skin lesions caused by leprosy; in 2006, the agency extended its approval of thalidomide to treat multiple myeloma.

Thomä and his colleagues got down to work of figuring out how thalidomide interacted with CRBN. “As often is the case in crystallography, it took the right construct, the right conditions and a little bit of luck,” says Thomä, to get the structures of thalidomide and drugs like it bound to a complex of chicken CRBN (the chicken version closely resembles the human one) and its adaptor protein.

The investigators showed that when thalidomide bound to CRBN the protein was prevented from binding to one of its targets, the homeobox transcription factor MEIS2. However, when CRBN was bound with thalidomide the protein was able to associate with a different class of transcription factors, called Ikaros. In short, thalidomide was able to divert the CRBN’s function to new substrates like Ikaros at the cost of losing MEIS2 and possibly other native substrates. Thomä stresses that the investigators still don’t know which substrate causes thalidomide’s ugly side effects.

Overall, the investigators concluded that “thalidomide simultaneously acts as antagonist and agonist on CRL4, something that was previously unanticipated,” says Thomä. “The unexpected complexity of thalidomide action, acting simultaneously as inhibitor and agonist on the ubiquitin ligase, provides a molecular framework for how small molecules can be used as drugs to up- or downregulate cellular targets.”

Telling apart psoriasis and eczema

July 9, 2014 § 1 Comment

Photo of a patient's skin who has psoriasis plaques in the center and eczema around the plaques. Photo courtesy of Kilian Eyerich.

Photo of a patient’s skin who has psoriasis plaques in the center and eczema around the plaques. Photo courtesy of Kilian Eyerich.

Eczema and psoriasis are chronic inflammatory skin diseases that sometimes are hard to tell apart because the irritated skin can look similar in both. Each condition requires a different kind of medical treatment. But when doctors can’t tell apart one condition from the other, it’s difficult for them to prescribe treatments, which can be expensive to undertake. Now, in a paper just out in the journal Science Translational Medicine, researchers have identified how the two conditions differ at the molecular level, which could guide clinicians in the future in telling the two skin diseases apart and prescribing treatment regimens.

Kilian and Stefanie Eyerich at the Technical University in Munich, Germany, know the frustrations of distinguishing between eczema and psoriasis firsthand.  “In our daily clinical practice, it is a common problem,” says Kilian Eyerich. “This is especially true for lesions on the hands, feet or scalp.”

The two investigators, who led the current study, noticed that some patients suffer from both psoriasis and eczema, with the manifestations of the two conditions sometimes appearing “just inches away from each other,” he says. He adds that this kind of patient is the “perfect model for us to investigate the pathogenesis of psoriasis and eczema” without the confounding factors of gender, age, genetics and environmental exposure.

The investigators recruited 24 patients who had both psoriasis and eczema and carried out polymerase chain reaction-based whole-genome expression analyses on unaffected skin, psoriasis lesions and eczema patches.

They found that psoriasis was mostly similar, on the molecular level, to a wound-healing reaction. The condition is known to be an immune response operating in overdrive in the outermost layer of the skin, causing scaly plaques. In contrast, eczema involved a different set of immune cells. These cells interfered with the epidermal barrier and the skin’s immune response. As a result, skin areas with eczema were susceptible to bacterial, fungal and viral infections, which inflame the skin even more.

Based on their results, the investigators zoomed in on two gene products, nitric oxide synthase 2 and the chemokine CCL27, which appeared to be specifically regulated in psoriasis. Eyerich says the expression levels of these two genes can help clinicians tell apart psoriasis and eczema. Indeed, in a different group of 53 patients, the investigators used these two genes to confirm diagnoses for some, provide new diagnoses and correct misdiagnoses.

Eyerich cautions that they need to reproduce their findings in larger groups of patients and use other molecular techniques, such as immunohistochemistry, to confirm their findings. But he hopes that the work will make an impact. “We hope this work will pave the way toward personalized medicine in inflammatory skin diseases,” he says. “We want to expand our investigation of the molecular signature of the diseases … to enable us to predict the perfect therapy for each individual patient based on his or her molecular signature in the future.”